From 010d82f55fa6d32258d5e15d72ceffe92bcb0d97 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 8 Jan 2025 14:24:17 +0100 Subject: [PATCH 01/25] Template update for nf-core/tools version 3.1.1 --- .editorconfig | 4 + .github/CONTRIBUTING.md | 24 +- .github/ISSUE_TEMPLATE/bug_report.yml | 1 - .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 38 +- .github/workflows/branch.yml | 18 +- .github/workflows/ci.yml | 59 ++- .github/workflows/download_pipeline.yml | 88 +++- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting.yml | 33 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 4 +- .../workflows/template_version_comment.yml | 46 ++ .gitignore | 1 + .gitpod.yml | 14 +- .nf-core.yml | 14 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + .vscode/settings.json | 3 + CITATIONS.md | 6 +- LICENSE | 2 +- README.md | 20 +- assets/schema_input.json | 2 +- conf/base.config | 36 +- conf/igenomes.config | 440 ------------------ conf/modules.config | 4 - conf/test.config | 16 +- conf/test_full.config | 4 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/output.md | 28 +- docs/usage.md | 47 +- main.nf | 21 - modules.json | 15 +- modules/nf-core/fastqc/environment.yml | 7 - modules/nf-core/fastqc/main.nf | 61 --- modules/nf-core/fastqc/meta.yml | 57 --- modules/nf-core/fastqc/tests/main.nf.test | 212 --------- .../nf-core/fastqc/tests/main.nf.test.snap | 88 ---- modules/nf-core/fastqc/tests/tags.yml | 2 - modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 16 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 24 +- modules/nf-core/multiqc/tests/nextflow.config | 5 + nextflow.config | 180 +++---- nextflow_schema.json | 115 +---- ro-crate-metadata.json | 311 +++++++++++++ .../utils_nfcore_references_pipeline/main.nf | 105 ++--- .../nf-core/utils_nextflow_pipeline/main.nf | 72 +-- .../tests/main.workflow.nf.test | 10 +- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 367 +++++++-------- .../tests/main.function.nf.test | 46 +- .../tests/main.function.nf.test.snap | 30 -- .../nf-core/utils_nfschema_plugin/main.nf | 46 ++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 +++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 --- .../utils_nfvalidation_plugin/meta.yml | 44 -- .../tests/main.nf.test | 200 -------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - workflows/references.nf | 30 +- 67 files changed, 1319 insertions(+), 2032 deletions(-) create mode 100644 .github/workflows/template_version_comment.yml create mode 100644 .vscode/settings.json delete mode 100644 conf/igenomes.config delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png delete mode 100644 modules/nf-core/fastqc/environment.yml delete mode 100644 modules/nf-core/fastqc/main.nf delete mode 100644 modules/nf-core/fastqc/meta.yml delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap delete mode 100644 modules/nf-core/fastqc/tests/tags.yml create mode 100644 modules/nf-core/multiqc/tests/nextflow.config create mode 100644 ro-crate-metadata.json create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 72dda289..6d9b74cc 100644 --- a/.editorconfig +++ b/.editorconfig @@ -31,3 +31,7 @@ indent_size = unset # ignore python and markdown [*.{py,md}] indent_style = unset + +# ignore ro-crate metadata files +[**/ro-crate-metadata.json] +insert_final_newline = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index e305f60e..51e96229 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,4 +1,4 @@ -# nf-core/references: Contributing Guidelines +# `nf-core/references`: Contributing Guidelines Hi there! Many thanks for taking an interest in improving nf-core/references. @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/references, the standard workflow i 1. Check that there isn't already an issue about your idea in the [nf-core/references issues](https://github.com/nf-core/references/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/references repository](https://github.com/nf-core/references) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -55,9 +55,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -- On your own fork, make a new branch `patch` based on `upstream/master`. +- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. - Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. +- Open a pull-request from `patch` to `main`/`master` with the changes. ## Getting help @@ -65,17 +65,17 @@ For further information/help, please consult the [nf-core/references documentati ## Pipeline contribution conventions -To make the nf-core/references code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. +To make the `nf-core/references` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. ### Adding a new step If you wish to contribute a new step, please use the following coding standards: -1. Define the corresponding input channel into your new process from the expected previous process channel +1. Define the corresponding input channel into your new process from the expected previous process channel. 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -84,13 +84,13 @@ If you wish to contribute a new step, please use the following coding standards: ### Default values -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. +Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index bd1f874d..023a2e9c 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,7 +9,6 @@ body: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [nf-core/references pipeline documentation](https://nf-co.re/references/usage) - - type: textarea id: description attributes: diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 83cd57eb..b322ee95 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/refe - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/references/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/references _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 21ad1ecd..ff4f1556 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,48 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the main/master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - main + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/references' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/references' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: + - name: Get PR reviews + uses: octokit/request-action@v2.x + if: github.event_name != 'workflow_dispatch' + id: check_approvals + continue-on-error: true + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + - name: Check for approvals + if: ${{ failure() && github.event_name != 'workflow_dispatch' }} + run: | + echo "No review approvals found. At least 2 approvals are required to run this action automatically." + exit 1 + + - name: Check for enough approvals (>=2) + id: test_variables + if: github.event_name != 'workflow_dispatch' + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index e408142c..705a8ecb 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,15 +1,17 @@ name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +# This workflow is triggered on PRs to `main`/`master` branch on the repository +# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: + - main + - master jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'nf-core/references' run: | @@ -22,7 +24,7 @@ jobs: uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | - ## This PR is against the `master` branch :x: + ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +34,9 @@ jobs: Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch. + The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8acbc999..707b5995 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,9 +7,12 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -17,30 +20,66 @@ concurrency: jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/references') }}" runs-on: ubuntu-latest strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: matrix.profile == 'singularity' + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge,bioconda + + - name: Set up Conda + if: matrix.profile == 'conda' + run: | + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d644..13b51e2c 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,14 +1,14 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main/master branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -17,17 +17,23 @@ on: - edited - synchronize branches: + - main - master pull_request_target: branches: + - main - master env: NXF_ANSI_LOG: false jobs: - download: + configure: runs-on: ubuntu-latest + outputs: + REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} + REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} + REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -35,13 +41,15 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -49,38 +57,74 @@ jobs: pip install git+https://github.com/nf-core/tools.git@dev - name: Get the repository name and current branch set as environment variable + id: get_repo_properties + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + + - name: Make a cache directory for the container images run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + mkdir -p ./singularity_container_images + download: + runs-on: ubuntu-latest + needs: configure + steps: - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" + + - name: Compare container image counts + run: | + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 2f407a0c..a1cbb03b 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe88..dbd52d5a 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" @@ -31,27 +31,42 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} @@ -59,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f..0bed96d3 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf7..450b1d5e 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: @@ -31,7 +31,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 00000000..537529bc --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,46 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + contains(env.OUTPUT, 'nf-core') + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitignore b/.gitignore index 5124c9ac..a42ce016 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ results/ testing/ testing* *.pyc +null/ diff --git a/.gitpod.yml b/.gitpod.yml index 105a1821..83599f63 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,7 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: - extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - charliermarsh.ruff # Code linter Ruff + extensions: + - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a77..debbf0c6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,14 @@ +nf_core_version: 3.1.1 repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: "@maxulysse" + description: help community build references + force: false + is_nfcore: true + name: references + org: nf-core + outdir: . + skip_features: + - fastqc + - igenomes + version: 1.0dev diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1dc..9e9f0e1c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.0.3" hooks: - id: editorconfig-checker alias: ec diff --git a/.prettierignore b/.prettierignore index 437d763d..edd29f01 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,3 +10,4 @@ testing/ testing* *.pyc bin/ +ro-crate-metadata.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..a33b527c --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "markdown.styles": ["public/vscode_markdown.css"] +} diff --git a/CITATIONS.md b/CITATIONS.md index 748c383d..504277b6 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,13 +10,9 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/LICENSE b/LICENSE index 897f9b7a..bf7cb796 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) @maxulysse +Copyright (c) The nf-core/references team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index d9656c0a..bcba19c3 100644 --- a/README.md +++ b/README.md @@ -3,13 +3,11 @@ nf-core/references - - -[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -29,15 +27,12 @@ - - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - - - + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/assets/schema_input.json b/assets/schema_input.json index ba2e2a05..fe91ae4b 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/references/master/assets/schema_input.json", "title": "nf-core/references pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index dd3c5534..ebfb6ddc 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,46 +11,46 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/igenomes.config b/conf/igenomes.config deleted file mode 100644 index 3f114377..00000000 --- a/conf/igenomes.config +++ /dev/null @@ -1,440 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines reference genomes using iGenome paths. - Can be used by any config that customises the base path using: - $params.igenomes_base / --igenomes_base ----------------------------------------------------------------------------------------- -*/ - -params { - // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} diff --git a/conf/modules.config b/conf/modules.config index d203d2b6..f0b0d55a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,10 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: FASTQC { - ext.args = '--quiet' - } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index 6091e939..8700be09 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,20 +10,22 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - // Genome references - genome = 'R64-1-1' + } diff --git a/conf/test_full.config b/conf/test_full.config index 69a35ddc..c31d49b3 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -19,6 +19,6 @@ params { // TODO nf-core: Give any required params for the test so that command line flags are not needed input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' - // Genome references - genome = 'R64-1-1' + // Fasta references + fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz' } diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e47acfb424dea1f326590d1eb2f6dfa26b5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 23458 zcmeFZ2UJtryD!S#x<#o93es(Ww4k)maRbte0-+a?-g^xY-3myTE`8G_KvA54)F1tn})nJ5u%TA4Y;^!^{48eL_}p#q-Umo0M|F1 z74+PQh^X8N|9_jcWbq~ 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s diff --git a/docs/output.md b/docs/output.md index 9def6aeb..0a40196e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,33 +12,9 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution -### FastQC - -
-Output files - -- `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. - -
- -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). - -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: - ### MultiQC
@@ -53,9 +29,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . - -### Pipeline information +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see .### Pipeline information
Output files diff --git a/docs/usage.md b/docs/usage.md index f6539b6f..eb869899 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/references --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run nf-core/references --input ./samplesheet.csv --outdir ./results -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -75,9 +75,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -85,12 +84,11 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/references -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' -genome: 'GRCh37' <...> ``` @@ -106,23 +104,21 @@ nextflow pull nf-core/references ### Reproducibility -It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. +It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. First, go to the [nf-core/references releases page](https://github.com/nf-core/references/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen) ### `-profile` @@ -130,16 +126,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!IMPORTANT] +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment. - `test` - A profile with a complete configuration for automated testing @@ -175,13 +170,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se ### Resource requests -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. +Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. ### Custom Containers -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. +In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. @@ -199,14 +194,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index ce0cfb7f..0a5037da 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -20,20 +18,6 @@ nextflow.enable.dsl = 2 include { REFERENCES } from './workflows/references' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_references_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_references_pipeline' - -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_references_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = getGenomeAttribute('fasta') - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -56,10 +40,8 @@ workflow NFCORE_REFERENCES { REFERENCES ( samplesheet ) - emit: multiqc_report = REFERENCES.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -70,13 +52,11 @@ workflow NFCORE_REFERENCES { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, @@ -90,7 +70,6 @@ workflow { NFCORE_REFERENCES ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index 4f8ee5df..e21083b3 100644 --- a/modules.json +++ b/modules.json @@ -5,14 +5,9 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "fastqc": { - "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", - "installed_by": ["modules"] - }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] } } @@ -21,17 +16,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml deleted file mode 100644 index 1787b38a..00000000 --- a/modules/nf-core/fastqc/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: fastqc -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index d79f1c86..00000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,61 +0,0 @@ -process FASTQC { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') - // FastQC memory value allowed range (100 - 10000) - def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) - - """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - $args \\ - --threads $task.cpus \\ - --memory $fastqc_memory \\ - $renamed_files - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index ee5507e0..00000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 70edae4d..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,212 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } - ) - } - } - - test("sarscov2 paired-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } - ) - } - } - - test("sarscov2 interleaved [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } - ) - } - } - - test("sarscov2 paired-end [bam]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } - ) - } - } - - test("sarscov2 multiple [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } - ) - } - } - - test("sarscov2 custom_prefix") { - - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } - ) - } - } - - test("sarscov2 single-end [fastq] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } - ) - } - } - -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index 86f7c311..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "fastqc_versions_interleaved": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:07.293713" - }, - "fastqc_stub": { - "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:31:01.425198" - }, - "fastqc_versions_multiple": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:55.797907" - }, - "fastqc_versions_bam": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:26.795862" - }, - "fastqc_versions_single": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:27.043675" - }, - "fastqc_versions_paired": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:47.584191" - }, - "fastqc_versions_custom_prefix": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:41:14.576531" - } -} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294b..00000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -44,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..2fcbb5ff 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-10-02T17:52:09.185842" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow.config b/nextflow.config index d4f633ea..80e7b2e7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,10 +12,6 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = false // MultiQC options multiqc_config = null @@ -33,48 +29,26 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - - // Config options + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/references custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/references.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/references profiles: ${params.custom_config_base}/pipeline/references.config") -} profiles { debug { dumpHashes = true @@ -89,7 +63,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -173,30 +147,36 @@ profiles { executor.name = 'local' executor.cpus = 4 executor.memory = 8.GB + process { + resourceLimits = [ + memory: 8.GB, + cpus : 4, + time : 1.h + ] + } } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" + +// Load nf-core/references custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/references.config" : "/dev/null" + +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' + -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} -// Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -208,73 +188,95 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html" } report { enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html" } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt" } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { name = 'nf-core/references' - author = """@maxulysse""" + author = """@maxulysse""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead + contributors = [ + // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 + [ + name: '@maxulysse', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + ] homePage = 'https://github.com/nf-core/references' description = """help community build references""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' + defaultBranch = 'master' + nextflowVersion = '!>=24.04.2' version = '1.0dev' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +validation { + defaultIgnoreParams = ["genomes"] + monochromeLogs = params.monochrome_logs + help { + enabled = true + command = "nextflow run nf-core/references -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m nf-core/references ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/references/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index d9898b6a..e4170b9f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/references/master/nextflow_schema.json", "title": "nf-core/references pipeline parameters", "description": "help community build references", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -43,37 +43,6 @@ } } }, - "reference_genome_options": { - "title": "Reference genome options", - "type": "object", - "fa_icon": "fas fa-dna", - "description": "Reference genome related files and options required for the workflow.", - "properties": { - "genome": { - "type": "string", - "description": "Name of iGenomes reference.", - "fa_icon": "fas fa-book", - "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." - }, - "fasta": { - "type": "string", - "format": "file-path", - "exists": true, - "mimetype": "text/plain", - "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", - "description": "Path to FASTA genome file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", - "fa_icon": "far fa-file-code" - }, - "igenomes_ignore": { - "type": "boolean", - "description": "Do not load the iGenomes reference config.", - "fa_icon": "fas fa-ban", - "hidden": true, - "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." - } - } - }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -122,41 +91,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -164,12 +98,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -245,52 +173,31 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", "hidden": true + }, + "trace_report_suffix": { + "type": "string", + "fa_icon": "far calendar", + "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", + "hidden": true } } } }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/reference_genome_options" - }, - { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json new file mode 100644 index 00000000..848ae20e --- /dev/null +++ b/ro-crate-metadata.json @@ -0,0 +1,311 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "GithubService": "https://w3id.org/ro/terms/test#GithubService", + "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", + "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", + "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", + "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", + "TestService": "https://w3id.org/ro/terms/test#TestService", + "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", + "TravisService": "https://w3id.org/ro/terms/test#TravisService", + "definition": "https://w3id.org/ro/terms/test#definition", + "engineVersion": "https://w3id.org/ro/terms/test#engineVersion", + "instance": "https://w3id.org/ro/terms/test#instance", + "resource": "https://w3id.org/ro/terms/test#resource", + "runsOn": "https://w3id.org/ro/terms/test#runsOn" + } + ], + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "creativeWorkStatus": "InProgress", + "datePublished": "2025-01-08T13:24:16+00:00", + "description": "

\n \n \n \"nf-core/references\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "hasPart": [ + { + "@id": "main.nf" + }, + { + "@id": "assets/" + }, + { + "@id": "conf/" + }, + { + "@id": "docs/" + }, + { + "@id": "docs/images/" + }, + { + "@id": "modules/" + }, + { + "@id": "modules/nf-core/" + }, + { + "@id": "workflows/" + }, + { + "@id": "subworkflows/" + }, + { + "@id": "nextflow.config" + }, + { + "@id": "README.md" + }, + { + "@id": "nextflow_schema.json" + }, + { + "@id": "CHANGELOG.md" + }, + { + "@id": "LICENSE" + }, + { + "@id": "CODE_OF_CONDUCT.md" + }, + { + "@id": "CITATIONS.md" + }, + { + "@id": "modules.json" + }, + { + "@id": "docs/usage.md" + }, + { + "@id": "docs/output.md" + }, + { + "@id": ".nf-core.yml" + }, + { + "@id": ".pre-commit-config.yaml" + }, + { + "@id": ".prettierignore" + } + ], + "isBasedOn": "https://github.com/nf-core/references", + "license": "MIT", + "mainEntity": { + "@id": "main.nf" + }, + "mentions": [ + { + "@id": "#3fccf3f2-6b03-4705-8813-ac11f8f5774d" + } + ], + "name": "nf-core/references" + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "main.nf", + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], + "dateCreated": "", + "dateModified": "2025-01-08T14:24:16Z", + "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "keywords": [ + "nf-core", + "nextflow" + ], + "license": [ + "MIT" + ], + "name": [ + "nf-core/references" + ], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "sdPublisher": { + "@id": "https://nf-co.re/" + }, + "url": [ + "https://github.com/nf-core/references", + "https://nf-co.re/references/dev/" + ], + "version": [ + "1.0dev" + ] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://www.nextflow.io/" + }, + "name": "Nextflow", + "url": { + "@id": "https://www.nextflow.io/" + }, + "version": "!>=24.04.2" + }, + { + "@id": "#3fccf3f2-6b03-4705-8813-ac11f8f5774d", + "@type": "TestSuite", + "instance": [ + { + "@id": "#7e306cef-1d0a-4391-a0f1-89d66d19c19c" + } + ], + "mainEntity": { + "@id": "main.nf" + }, + "name": "Test suite for nf-core/references" + }, + { + "@id": "#7e306cef-1d0a-4391-a0f1-89d66d19c19c", + "@type": "TestInstance", + "name": "GitHub Actions workflow for testing nf-core/references", + "resource": "repos/nf-core/references/actions/workflows/ci.yml", + "runsOn": { + "@id": "https://w3id.org/ro/terms/test#GithubService" + }, + "url": "https://api.github.com" + }, + { + "@id": "https://w3id.org/ro/terms/test#GithubService", + "@type": "TestService", + "name": "Github Actions", + "url": { + "@id": "https://github.com" + } + }, + { + "@id": "assets/", + "@type": "Dataset", + "description": "Additional files" + }, + { + "@id": "conf/", + "@type": "Dataset", + "description": "Configuration files" + }, + { + "@id": "docs/", + "@type": "Dataset", + "description": "Markdown files for documenting the pipeline" + }, + { + "@id": "docs/images/", + "@type": "Dataset", + "description": "Images for the documentation files" + }, + { + "@id": "modules/", + "@type": "Dataset", + "description": "Modules used by the pipeline" + }, + { + "@id": "modules/nf-core/", + "@type": "Dataset", + "description": "nf-core modules" + }, + { + "@id": "workflows/", + "@type": "Dataset", + "description": "Main pipeline workflows to be executed in main.nf" + }, + { + "@id": "subworkflows/", + "@type": "Dataset", + "description": "Smaller subworkflows" + }, + { + "@id": "nextflow.config", + "@type": "File", + "description": "Main Nextflow configuration file" + }, + { + "@id": "README.md", + "@type": "File", + "description": "Basic pipeline usage information" + }, + { + "@id": "nextflow_schema.json", + "@type": "File", + "description": "JSON schema for pipeline parameter specification" + }, + { + "@id": "CHANGELOG.md", + "@type": "File", + "description": "Information on changes made to the pipeline" + }, + { + "@id": "LICENSE", + "@type": "File", + "description": "The license - should be MIT" + }, + { + "@id": "CODE_OF_CONDUCT.md", + "@type": "File", + "description": "The nf-core code of conduct" + }, + { + "@id": "CITATIONS.md", + "@type": "File", + "description": "Citations needed when using the pipeline" + }, + { + "@id": "modules.json", + "@type": "File", + "description": "Version information for modules from nf-core/modules" + }, + { + "@id": "docs/usage.md", + "@type": "File", + "description": "Usage documentation" + }, + { + "@id": "docs/output.md", + "@type": "File", + "description": "Output documentation" + }, + { + "@id": ".nf-core.yml", + "@type": "File", + "description": "nf-core configuration file, configuring template features and linting rules" + }, + { + "@id": ".pre-commit-config.yaml", + "@type": "File", + "description": "Configuration file for pre-commit hooks" + }, + { + "@id": ".prettierignore", + "@type": "File", + "description": "Ignore file for prettier" + }, + { + "@id": "https://nf-co.re/", + "@type": "Organization", + "name": "nf-core", + "url": "https://nf-co.re/" + } + ] +} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_references_pipeline/main.nf b/subworkflows/local/utils_nfcore_references_pipeline/main.nf index e37808f7..124ac823 100644 --- a/subworkflows/local/utils_nfcore_references_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_references_pipeline/main.nf @@ -8,29 +8,25 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -54,16 +50,10 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) // @@ -72,16 +62,13 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) - // - // Custom validation for pipeline parameters - // - validateInputParameters() // // Create channel from input file provided through params.input // + Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -91,8 +78,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { - validateInputSamplesheet(it) + .map { samplesheet -> + validateInputSamplesheet(samplesheet) } .map { meta, fastqs -> @@ -106,9 +93,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -123,19 +110,26 @@ workflow PIPELINE_COMPLETION { multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def multiqc_reports = multiqc_report.toList() // // Completion email and summary // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_reports.getVal(), + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -147,16 +141,10 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// Check and validate pipeline parameters -// -def validateInputParameters() { - genomeExistsError() -} // // Validate channels from input samplesheet @@ -165,39 +153,13 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } return [ metas[0], fastqs ] } -// -// Get attribute from genome config file e.g. fasta -// -def getGenomeAttribute(attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null -} - -// -// Exit pipeline if incorrect --genome key provided -// -def genomeExistsError() { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - error(error_string) - } -} - // // Generate methods description for MultiQC // @@ -207,7 +169,6 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "FastQC (Andrews 2010),", "MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -220,7 +181,6 @@ def toolBibliographyText() { // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " ].join(' ').trim() @@ -228,7 +188,7 @@ def toolBibliographyText() { } def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = workflow.toMap() meta["manifest_map"] = workflow.manifest.toMap() @@ -239,8 +199,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi:     ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -261,3 +223,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f..d6e593e8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,18 +2,13 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -76,13 +71,13 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,37 +85,42 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf..a09572e5 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c39..bfd25876 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,17 +2,13 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -25,23 +21,20 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -52,39 +45,22 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +78,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -113,8 +89,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -122,11 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { processVersionsFromYAML(it) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -134,61 +106,40 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -200,79 +151,76 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - return mqc_report } // @@ -281,26 +229,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -317,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -337,40 +294,45 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -378,15 +340,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") + } + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -395,21 +359,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -434,13 +407,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f8..f117040c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232c..02c67014 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000..4994303e --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000..f7d9f028 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000..8fb30164 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000..0907ac58 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c9..331e0d2f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65d..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33f..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/references.nf b/workflows/references.nf index 3286a4e6..1abafc63 100644 --- a/workflows/references.nf +++ b/workflows/references.nf @@ -3,10 +3,8 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - -include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_references_pipeline' @@ -21,32 +19,23 @@ workflow REFERENCES { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() - // - // MODULE: Run FastQC - // - FASTQC ( - ch_samplesheet - ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - // // Collate and save software versions // softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'nf_core_' + 'references_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } + // // MODULE: MultiQC // @@ -62,15 +51,14 @@ workflow REFERENCES { summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -83,12 +71,14 @@ workflow REFERENCES { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + } /* From 0ee36c54eaa5c2ed05e123c649718ac4864b3ff7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 16:02:45 +0100 Subject: [PATCH 02/25] Template update for nf-core/tools version 3.2.0 --- .github/workflows/ci.yml | 2 ++ .github/workflows/download_pipeline.yml | 28 +++++++++------- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 33 ------------------- .nf-core.yml | 10 +++++- .pre-commit-config.yaml | 2 +- README.md | 10 ++++-- conf/test.config | 2 -- docs/output.md | 4 ++- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +-- .../nf-core/multiqc/tests/main.nf.test.snap | 24 +++++++------- nextflow.config | 18 +++++----- ro-crate-metadata.json | 19 ++++++----- 15 files changed, 75 insertions(+), 87 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 707b5995..207fdcbc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,6 +46,8 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 13b51e2c..ab06316e 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -34,6 +34,17 @@ jobs: REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} + steps: + - name: Get the repository name and current branch + id: get_repo_properties + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + + download: + runs-on: ubuntu-latest + needs: configure steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -56,21 +67,10 @@ jobs: python -m pip install --upgrade pip pip install git+https://github.com/nf-core/tools.git@dev - - name: Get the repository name and current branch set as environment variable - id: get_repo_properties - run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" - - name: Make a cache directory for the container images run: | mkdir -p ./singularity_container_images - download: - runs-on: ubuntu-latest - needs: configure - steps: - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images @@ -87,6 +87,9 @@ jobs: - name: Inspect download run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + - name: Count the downloaded number of container images id: count_initial run: | @@ -123,7 +126,8 @@ jobs: final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} difference=$((final_count - initial_count)) echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" - tree ./singularity_container_images + tree ./singularity_container_images > ./container_afterwards + diff ./container_initial ./container_afterwards exit 1 else echo "The pipeline can be downloaded successfully!" diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 0bed96d3..95b6b6af 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 + uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 450b1d5e..76a9e67e 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -27,39 +27,6 @@ jobs: ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics - send-tweet: - runs-on: ubuntu-latest - - steps: - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy - - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} - bsky-post: runs-on: ubuntu-latest steps: diff --git a/.nf-core.yml b/.nf-core.yml index debbf0c6..dbe2cb14 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,12 @@ -nf_core_version: 3.1.1 +lint: + actions_awsfulltest: false + files_exist: + - conf/igenomes.config + - conf/igenomes_ignored.config + files_unchanged: + - .github/workflows/branch.yml + - .github/workflows/linting.yml +nf_core_version: 3.2.0 repository_type: pipeline template: author: "@maxulysse" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9e9f0e1c..1dec8650 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.0.3" + rev: "3.1.2" hooks: - id: editorconfig-checker alias: ec diff --git a/README.md b/README.md index bcba19c3..e4bc4b51 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ nf-core/references -[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml) + + +[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) @@ -32,7 +34,7 @@ ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - + + + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/conf/test.config b/conf/test.config index 8700be09..325d34c9 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,6 +26,4 @@ params { // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - } diff --git a/docs/output.md b/docs/output.md index 0a40196e..52d3ffd8 100644 --- a/docs/output.md +++ b/docs/output.md @@ -29,7 +29,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see .### Pipeline information +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . + +### Pipeline information
    Output files diff --git a/modules.json b/modules.json index e21083b3..94d156a6 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", "installed_by": ["modules"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 6f5b867b..a27122ce 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.25.1 + - bioconda::multiqc=1.27 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index cc0643e1..58d9313c 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : + 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 2fcbb5ff..7b7c1322 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:51:46.317523" + "timestamp": "2025-01-27T09:29:57.631982377" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:20.680978" + "timestamp": "2025-01-27T09:30:34.743726958" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:09.185842" + "timestamp": "2025-01-27T09:30:21.44383553" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 80e7b2e7..f2660a64 100644 --- a/nextflow.config +++ b/nextflow.config @@ -189,14 +189,14 @@ env { } // Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -243,7 +243,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 848ae20e..65251f5b 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-01-08T13:24:16+00:00", - "description": "

    \n \n \n \"nf-core/references\"\n \n

    [![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-02-27T15:02:40+00:00", + "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#3fccf3f2-6b03-4705-8813-ac11f8f5774d" + "@id": "#f2c008e4-ad40-48dc-99e4-e4b39439bec9" } ], "name": "nf-core/references" @@ -127,11 +127,14 @@ "ComputationalWorkflow" ], "dateCreated": "", - "dateModified": "2025-01-08T14:24:16Z", + "dateModified": "2025-02-27T16:02:40Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", - "nextflow" + "nextflow", + "genome", + "references", + "reproducibility" ], "license": [ "MIT" @@ -166,11 +169,11 @@ "version": "!>=24.04.2" }, { - "@id": "#3fccf3f2-6b03-4705-8813-ac11f8f5774d", + "@id": "#f2c008e4-ad40-48dc-99e4-e4b39439bec9", "@type": "TestSuite", "instance": [ { - "@id": "#7e306cef-1d0a-4391-a0f1-89d66d19c19c" + "@id": "#934dc31c-693d-4c65-aa48-938f3eb44a9f" } ], "mainEntity": { @@ -179,7 +182,7 @@ "name": "Test suite for nf-core/references" }, { - "@id": "#7e306cef-1d0a-4391-a0f1-89d66d19c19c", + "@id": "#934dc31c-693d-4c65-aa48-938f3eb44a9f", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/references", "resource": "repos/nf-core/references/actions/workflows/ci.yml", From 813cefb0da2e7c154b187e93b5792797b3d3c2bf Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 30 Apr 2025 16:56:39 +0200 Subject: [PATCH 03/25] Template update for nf-core/tools version 3.2.1 --- .github/workflows/awsfulltest.yml | 41 ++++++++----------------------- .github/workflows/ci.yml | 1 + .nf-core.yml | 5 ++-- nextflow.config | 2 +- ro-crate-metadata.json | 12 ++++----- 5 files changed, 21 insertions(+), 40 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index ff4f1556..40bfcc57 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -4,44 +4,23 @@ name: nf-core AWS full size tests # It runs the -profile 'test_full' on AWS batch on: - pull_request: - branches: - - main - - master workflow_dispatch: pull_request_review: types: [submitted] + release: + types: [published] jobs: run-platform: name: Run AWS full tests - # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered - if: github.repository == 'nf-core/references' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' + # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered + if: github.repository == 'nf-core/references' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - - name: Get PR reviews - uses: octokit/request-action@v2.x - if: github.event_name != 'workflow_dispatch' - id: check_approvals - continue-on-error: true - with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - - name: Check for approvals - if: ${{ failure() && github.event_name != 'workflow_dispatch' }} - run: | - echo "No review approvals found. At least 2 approvals are required to run this action automatically." - exit 1 - - - name: Check for enough approvals (>=2) - id: test_variables - if: github.event_name != 'workflow_dispatch' + - name: Set revision variable + id: revision run: | - JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' - CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') - test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required + echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 @@ -52,12 +31,12 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/references/work-${{ github.sha }} + revision: ${{ steps.revision.outputs.revision }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/references/work-${{ steps.revision.outputs.revision }} parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/references/results-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/references/results-${{ steps.revision.outputs.revision }}" } profiles: test_full diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 207fdcbc..04a5b945 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -83,5 +83,6 @@ jobs: uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} run: | nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.nf-core.yml b/.nf-core.yml index dbe2cb14..e057a278 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,12 +1,13 @@ lint: actions_awsfulltest: false files_exist: + - .github/workflows/ci.yml - conf/igenomes.config - conf/igenomes_ignored.config files_unchanged: - - .github/workflows/branch.yml + - .github/PULL_REQUEST_TEMPLATE.md - .github/workflows/linting.yml -nf_core_version: 3.2.0 +nf_core_version: 3.2.1 repository_type: pipeline template: author: "@maxulysse" diff --git a/nextflow.config b/nextflow.config index f2660a64..ce2fddb9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -243,7 +243,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 65251f5b..a0de433d 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-02-27T15:02:40+00:00", + "datePublished": "2025-04-30T14:56:37+00:00", "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#f2c008e4-ad40-48dc-99e4-e4b39439bec9" + "@id": "#482e6c4f-a3a9-4f7d-ac71-db8cd15037a1" } ], "name": "nf-core/references" @@ -127,7 +127,7 @@ "ComputationalWorkflow" ], "dateCreated": "", - "dateModified": "2025-02-27T16:02:40Z", + "dateModified": "2025-04-30T16:56:37Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -169,11 +169,11 @@ "version": "!>=24.04.2" }, { - "@id": "#f2c008e4-ad40-48dc-99e4-e4b39439bec9", + "@id": "#482e6c4f-a3a9-4f7d-ac71-db8cd15037a1", "@type": "TestSuite", "instance": [ { - "@id": "#934dc31c-693d-4c65-aa48-938f3eb44a9f" + "@id": "#8041a945-88f2-4a29-b730-f7cd8c5c752d" } ], "mainEntity": { @@ -182,7 +182,7 @@ "name": "Test suite for nf-core/references" }, { - "@id": "#934dc31c-693d-4c65-aa48-938f3eb44a9f", + "@id": "#8041a945-88f2-4a29-b730-f7cd8c5c752d", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/references", "resource": "repos/nf-core/references/actions/workflows/ci.yml", From ff7e34735e48975140ca3b87d2310bd1302f6d2d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 14 Jul 2025 11:36:09 +0200 Subject: [PATCH 04/25] Template update for nf-core/tools version 3.3.2 --- .editorconfig | 37 ----- .github/CONTRIBUTING.md | 2 +- .github/actions/get-shards/action.yml | 69 +++++++++ .github/actions/nf-test/action.yml | 109 +++++++++++++ .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 2 +- .github/workflows/ci.yml | 88 ----------- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 20 +-- .../{fix-linting.yml => fix_linting.yml} | 4 +- .github/workflows/linting.yml | 17 +-- .github/workflows/linting_comment.yml | 4 +- .github/workflows/nf-test.yml | 143 ++++++++++++++++++ .github/workflows/release-announcements.yml | 2 +- ...mment.yml => template-version-comment.yml} | 2 +- .nf-core.yml | 5 +- .pre-commit-config.yaml | 26 +++- .prettierrc.yml | 5 + README.md | 9 +- assets/schema_input.json | 4 +- conf/base.config | 6 +- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/meta.yml | 110 ++++++++------ .../nf-core/multiqc/tests/main.nf.test.snap | 18 +-- nextflow.config | 20 ++- nf-test.config | 24 +++ ro-crate-metadata.json | 18 +-- .../utils_nfcore_references_pipeline/main.nf | 1 - .../tests/nextflow.config | 2 +- tests/.nftignore | 9 ++ tests/default.nf.test | 35 +++++ tests/nextflow.config | 14 ++ 34 files changed, 573 insertions(+), 248 deletions(-) delete mode 100644 .editorconfig create mode 100644 .github/actions/get-shards/action.yml create mode 100644 .github/actions/nf-test/action.yml delete mode 100644 .github/workflows/ci.yml rename .github/workflows/{fix-linting.yml => fix_linting.yml} (96%) create mode 100644 .github/workflows/nf-test.yml rename .github/workflows/{template_version_comment.yml => template-version-comment.yml} (95%) create mode 100644 nf-test.config create mode 100644 tests/.nftignore create mode 100644 tests/default.nf.test create mode 100644 tests/nextflow.config diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 6d9b74cc..00000000 --- a/.editorconfig +++ /dev/null @@ -1,37 +0,0 @@ -root = true - -[*] -charset = utf-8 -end_of_line = lf -insert_final_newline = true -trim_trailing_whitespace = true -indent_size = 4 -indent_style = space - -[*.{md,yml,yaml,html,css,scss,js}] -indent_size = 2 - -# These files are edited and tested upstream in nf-core/modules -[/modules/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset -[/subworkflows/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset - -[/assets/email*] -indent_size = unset - -# ignore python and markdown -[*.{py,md}] -indent_style = unset - -# ignore ro-crate metadata files -[**/ro-crate-metadata.json] -insert_final_newline = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 51e96229..358d2650 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -78,7 +78,7 @@ If you wish to contribute a new step, please use the following coding standards: 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test command in `.github/workflow/ci.yml`. +8. If applicable, add a new test in the `tests` directory. 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml new file mode 100644 index 00000000..34085279 --- /dev/null +++ b/.github/actions/get-shards/action.yml @@ -0,0 +1,69 @@ +name: "Get number of shards" +description: "Get the number of nf-test shards for the current CI job" +inputs: + max_shards: + description: "Maximum number of shards allowed" + required: true + paths: + description: "Component paths to test" + required: false + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: false +outputs: + shard: + description: "Array of shard numbers" + value: ${{ steps.shards.outputs.shard }} + total_shards: + description: "Total number of shards" + value: ${{ steps.shards.outputs.total_shards }} +runs: + using: "composite" + steps: + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFT_VER }} + - name: Get number of shards + id: shards + shell: bash + run: | + # Run nf-test with dynamic parameter + nftest_output=$(nf-test test \ + --profile +docker \ + $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ + --dry-run \ + --ci \ + --changed-since HEAD^) || { + echo "nf-test command failed with exit code $?" + echo "Full output: $nftest_output" + exit 1 + } + echo "nf-test dry-run output: $nftest_output" + + # Default values for shard and total_shards + shard="[]" + total_shards=0 + + # Check if there are related tests + if echo "$nftest_output" | grep -q 'No tests to execute'; then + echo "No related tests found." + else + # Extract the number of related tests + number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p') + if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then + shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} )) + shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .) + total_shards="$shards_to_run" + else + echo "Unexpected output format. Falling back to default values." + fi + fi + + # Write to GitHub Actions outputs + echo "shard=$shard" >> $GITHUB_OUTPUT + echo "total_shards=$total_shards" >> $GITHUB_OUTPUT + + # Debugging output + echo "Final shard array: $shard" + echo "Total number of shards: $total_shards" diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml new file mode 100644 index 00000000..bf44d961 --- /dev/null +++ b/.github/actions/nf-test/action.yml @@ -0,0 +1,109 @@ +name: "nf-test Action" +description: "Runs nf-test with common setup steps" +inputs: + profile: + description: "Profile to use" + required: true + shard: + description: "Shard number for this CI job" + required: true + total_shards: + description: "Total number of test shards(NOT the total number of matrix jobs)" + required: true + paths: + description: "Test paths" + required: true + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: false +runs: + using: "composite" + steps: + - name: Setup Nextflow + uses: nf-core/setup-nextflow@v2 + with: + version: "${{ env.NXF_VERSION }}" + + - name: Set up Python + uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + with: + python-version: "3.13" + + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + with: + version: "${{ env.NFT_VER }}" + install-pdiff: true + + - name: Setup apptainer + if: contains(inputs.profile, 'singularity') + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: contains(inputs.profile, 'singularity') + shell: bash + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Conda setup + if: contains(inputs.profile, 'conda') + uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3 + with: + auto-update-conda: true + conda-solver: libmamba + conda-remove-defaults: true + + - name: Run nf-test + shell: bash + env: + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + run: | + nf-test test \ + --profile=+${{ inputs.profile }} \ + $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ + --ci \ + --changed-since HEAD^ \ + --verbose \ + --tap=test.tap \ + --shard ${{ inputs.shard }}/${{ inputs.total_shards }} + + # Save the absolute path of the test.tap file to the output + echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT + + - name: Generate test summary + if: always() + shell: bash + run: | + # Add header if it doesn't exist (using a token file to track this) + if [ ! -f ".summary_header" ]; then + echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY + echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY + touch .summary_header + fi + + if [ -f test.tap ]; then + while IFS= read -r line; do + if [[ $line =~ ^ok ]]; then + test_name="${line#ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + elif [[ $line =~ ^not\ ok ]]; then + test_name="${line#not ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + done < test.tap + else + echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + + - name: Clean up + if: always() + shell: bash + run: | + sudo rm -rf /home/ubuntu/tests/ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 40bfcc57..2b1f3e60 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: run-platform: name: Run AWS full tests # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered - if: github.repository == 'nf-core/references' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' + if: github.repository == 'nf-core/references' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release' runs-on: ubuntu-latest steps: - name: Set revision variable @@ -40,7 +40,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 6c92d598..e1b779ff 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 04a5b945..00000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,88 +0,0 @@ -name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors -on: - push: - branches: - - dev - pull_request: - release: - types: [published] - workflow_dispatch: - -env: - NXF_ANSI_LOG: false - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - -concurrency: - group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: true - -jobs: - test: - name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/references') }}" - runs-on: ubuntu-latest - strategy: - matrix: - NXF_VER: - - "24.04.2" - - "latest-everything" - profile: - - "conda" - - "docker" - - "singularity" - test_name: - - "test" - isMaster: - - ${{ github.base_ref == 'master' }} - # Exclude conda and singularity on dev - exclude: - - isMaster: false - profile: "conda" - - isMaster: false - profile: "singularity" - steps: - - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - with: - fetch-depth: 0 - - - name: Set up Nextflow - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Set up Apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - - name: Clean up Disk space - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" - continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} - run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 0b6b1f27..ac030fd5 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 + - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index ab06316e..999bcc38 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -12,14 +12,6 @@ on: required: true default: "dev" pull_request: - types: - - opened - - edited - - synchronize - branches: - - main - - master - pull_request_target: branches: - main - master @@ -52,9 +44,9 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: - python-version: "3.12" + python-version: "3.13" architecture: "x64" - name: Setup Apptainer @@ -120,6 +112,7 @@ jobs: echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts + id: count_comparison run: | if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} @@ -132,3 +125,10 @@ jobs: else echo "The pipeline can be downloaded successfully!" fi + + - name: Upload Nextflow logfile for debugging purposes + uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + with: + name: nextflow_logfile.txt + path: .nextflow.log* + include-hidden-files: true diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml similarity index 96% rename from .github/workflows/fix-linting.yml rename to .github/workflows/fix_linting.yml index a1cbb03b..23e74651 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix_linting.yml @@ -32,9 +32,9 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: - python-version: "3.12" + python-version: "3.13" - name: Install pre-commit run: pip install pre-commit diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index dbd52d5a..8b0f88c3 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -3,9 +3,6 @@ name: nf-core linting # It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: - push: - branches: - - dev pull_request: release: types: [published] @@ -16,10 +13,10 @@ jobs: steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - name: Set up Python 3.12 - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - name: Set up Python 3.13 + uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: - python-version: "3.12" + python-version: "3.13" - name: Install pre-commit run: pip install pre-commit @@ -36,13 +33,13 @@ jobs: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: - python-version: "3.12" + python-version: "3.13" architecture: "x64" - name: read .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.1.0 + uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml @@ -74,7 +71,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 + uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 95b6b6af..d43797d9 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 + uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 + uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml new file mode 100644 index 00000000..e7b58449 --- /dev/null +++ b/.github/workflows/nf-test.yml @@ -0,0 +1,143 @@ +name: Run nf-test +on: + pull_request: + paths-ignore: + - "docs/**" + - "**/meta.yml" + - "**/*.md" + - "**/*.png" + - "**/*.svg" + release: + types: [published] + workflow_dispatch: + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + NFT_VER: "0.9.2" + NFT_WORKDIR: "~" + NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + +jobs: + nf-test-changes: + name: nf-test-changes + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test-changes + - runner=4cpu-linux-x64 + outputs: + shard: ${{ steps.set-shards.outputs.shard }} + total_shards: ${{ steps.set-shards.outputs.total_shards }} + steps: + - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner + run: | + ls -la ./ + rm -rf ./* || true + rm -rf ./.??* || true + ls -la ./ + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 + + - name: get number of shards + id: set-shards + uses: ./.github/actions/get-shards + env: + NFT_VER: ${{ env.NFT_VER }} + with: + max_shards: 7 + + - name: debug + run: | + echo ${{ steps.set-shards.outputs.shard }} + echo ${{ steps.set-shards.outputs.total_shards }} + + nf-test: + name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" + needs: [nf-test-changes] + if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test + - runner=4cpu-linux-x64 + strategy: + fail-fast: false + matrix: + shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} + profile: [conda, docker, singularity] + isMain: + - ${{ github.base_ref == 'master' || github.base_ref == 'main' }} + # Exclude conda and singularity on dev + exclude: + - isMain: false + profile: "conda" + - isMain: false + profile: "singularity" + NXF_VER: + - "24.10.5" + - "latest-everything" + env: + NXF_ANSI_LOG: false + TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} + + steps: + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 + + - name: Run nf-test + id: run_nf_test + uses: ./.github/actions/nf-test + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} + env: + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + with: + profile: ${{ matrix.profile }} + shard: ${{ matrix.shard }} + total_shards: ${{ env.TOTAL_SHARDS }} + + - name: Report test status + if: ${{ always() }} + run: | + if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then + echo "::error::Test with ${{ matrix.NXF_VER }} failed" + # Add to workflow summary + echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY + if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then + echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." + fi + if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + exit 1 + fi + fi + + confirm-pass: + needs: [nf-test] + if: always() + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-confirm-pass + - runner=2cpu-linux-x64 + steps: + - name: One or more tests failed (excluding latest-everything) + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 + + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + + - name: debug-print + if: always() + run: | + echo "::group::DEBUG: `needs` Contents" + echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" + echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" + echo "::endgroup::" diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 76a9e67e..0f732495 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -30,7 +30,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 + - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml similarity index 95% rename from .github/workflows/template_version_comment.yml rename to .github/workflows/template-version-comment.yml index 537529bc..beb5c77f 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -14,7 +14,7 @@ jobs: ref: ${{ github.event.pull_request.head.sha }} - name: Read template version from .nf-core.yml - uses: nichmor/minimal-read-yaml@v0.0.2 + uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml diff --git a/.nf-core.yml b/.nf-core.yml index e057a278..b31e7002 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -7,7 +7,10 @@ lint: files_unchanged: - .github/PULL_REQUEST_TEMPLATE.md - .github/workflows/linting.yml -nf_core_version: 3.2.1 + - assets/nf-core-references_logo_light.png + - docs/images/nf-core-references_logo_light.png + - docs/images/nf-core-references_logo_dark.png +nf_core_version: 3.3.2 repository_type: pipeline template: author: "@maxulysse" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1dec8650..bb41beec 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,10 +4,24 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.2.5 - - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.1.2" + - prettier@3.6.2 + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 hooks: - - id: editorconfig-checker - alias: ec + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/nf-core/.*| + subworkflows/nf-core/.*| + .*\.snap$ + )$ + - id: end-of-file-fixer + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/nf-core/.*| + subworkflows/nf-core/.*| + .*\.snap$ + )$ diff --git a/.prettierrc.yml b/.prettierrc.yml index c81f9a76..07dbd8bb 100644 --- a/.prettierrc.yml +++ b/.prettierrc.yml @@ -1 +1,6 @@ printWidth: 120 +tabWidth: 4 +overrides: + - files: "*.{md,yml,yaml,html,css,scss,js,cff}" + options: + tabWidth: 2 diff --git a/README.md b/README.md index e4bc4b51..13e0006b 100644 --- a/README.md +++ b/README.md @@ -5,17 +5,18 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction @@ -28,7 +29,7 @@ --> + workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples. --> 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage diff --git a/assets/schema_input.json b/assets/schema_input.json index fe91ae4b..98ff18f4 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -17,14 +17,14 @@ "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, diff --git a/conf/base.config b/conf/base.config index ebfb6ddc..39f65c68 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' @@ -59,4 +59,8 @@ process { errorStrategy = 'retry' maxRetries = 2 } + withLabel: process_gpu { + ext.use_gpu = { workflow.profile.contains('gpu') } + accelerator = { workflow.profile.contains('gpu') ? 1 : null } + } } diff --git a/modules.json b/modules.json index 94d156a6..62fb0a84 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122ce..812fc4c5 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.27 + - bioconda::multiqc=1.29 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 58d9313c..0ac3c369 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : - 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : + 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index b16c1879..ce30eb73 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -15,57 +15,71 @@ tools: licence: ["GPL-3.0-or-later"] identifier: biotools:multiqc input: - - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - - - multiqc_logo: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + ontologies: [] + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + ontologies: [] + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV +output: + report: + - "*multiqc_report.html": type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - - replace_names: + description: MultiQC report file + pattern: "multiqc_report.html" + ontologies: [] + data: + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - "*_plots": type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - - sample_names: + description: Plots created by MultiQC + pattern: "*_data" + ontologies: [] + versions: + - versions.yml: type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" -output: - - report: - - "*multiqc_report.html": - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - - "*_plots": - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7b7c1322..88e90571 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:29:57.631982377" + "timestamp": "2025-05-22T11:50:41.182332996" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:34.743726958" + "timestamp": "2025-05-22T11:51:22.448739369" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:21.44383553" + "timestamp": "2025-05-22T11:51:06.198928424" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index ce2fddb9..fe6b64b1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -155,16 +155,25 @@ profiles { ] } } + gpu { + docker.runOptions = '-u $(id -u):$(id -g) --gpus all' + apptainer.runOptions = '--nv' + singularity.runOptions = '--nv' + } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } -// Load nf-core custom profiles from different Institutions -includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" +// Load nf-core custom profiles from different institutions + +// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. +// Load nf-core/references custom profiles from different institutions. +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" + // Load nf-core/references custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/references.config" : "/dev/null" +// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/references.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled @@ -220,7 +229,6 @@ dag { manifest { name = 'nf-core/references' - author = """@maxulysse""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ @@ -236,14 +244,14 @@ manifest { description = """help community build references""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=24.04.2' + nextflowVersion = '!>=24.10.5' version = '1.0dev' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..3a1fff59 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,24 @@ +config { + // location for all nf-test tests + testsDir "." + + // nf-test directory including temporary files for each test + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + + // location of an optional nextflow.config file specific for executing tests + configFile "tests/nextflow.config" + + // ignore tests coming from the nf-core/modules repo + ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' + + // run all test with defined profile(s) from the main nextflow.config + profile "test" + + // list of filenames or patterns that should be trigger a full test run + triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' + + // load the necessary plugins + plugins { + load "nft-utils@0.0.3" + } +} diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index a0de433d..dea54367 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-04-30T14:56:37+00:00", - "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-07-14T09:36:06+00:00", + "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#482e6c4f-a3a9-4f7d-ac71-db8cd15037a1" + "@id": "#7013769a-0bdc-4319-8311-26037f814cf4" } ], "name": "nf-core/references" @@ -127,7 +127,7 @@ "ComputationalWorkflow" ], "dateCreated": "", - "dateModified": "2025-04-30T16:56:37Z", + "dateModified": "2025-07-14T11:36:06Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -166,14 +166,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.04.2" + "version": "!>=24.10.5" }, { - "@id": "#482e6c4f-a3a9-4f7d-ac71-db8cd15037a1", + "@id": "#7013769a-0bdc-4319-8311-26037f814cf4", "@type": "TestSuite", "instance": [ { - "@id": "#8041a945-88f2-4a29-b730-f7cd8c5c752d" + "@id": "#68c4672c-6c98-4bb0-bc81-e5cd34d66762" } ], "mainEntity": { @@ -182,10 +182,10 @@ "name": "Test suite for nf-core/references" }, { - "@id": "#8041a945-88f2-4a29-b730-f7cd8c5c752d", + "@id": "#68c4672c-6c98-4bb0-bc81-e5cd34d66762", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/references", - "resource": "repos/nf-core/references/actions/workflows/ci.yml", + "resource": "repos/nf-core/references/actions/workflows/nf-test.yml", "runsOn": { "@id": "https://w3id.org/ro/terms/test#GithubService" }, diff --git a/subworkflows/local/utils_nfcore_references_pipeline/main.nf b/subworkflows/local/utils_nfcore_references_pipeline/main.nf index 124ac823..378a230f 100644 --- a/subworkflows/local/utils_nfcore_references_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_references_pipeline/main.nf @@ -223,4 +223,3 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 0907ac58..09ef842a 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.1.0" + id "nf-schema@2.4.2" } validation { diff --git a/tests/.nftignore b/tests/.nftignore new file mode 100644 index 00000000..16409f40 --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,9 @@ +.DS_Store +multiqc/multiqc_data/BETA-multiqc.parquet +multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_data.json +multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} +multiqc/multiqc_report.html +pipeline_info/*.{html,json,txt,yml} diff --git a/tests/default.nf.test b/tests/default.nf.test new file mode 100644 index 00000000..8a2e92c9 --- /dev/null +++ b/tests/default.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + + test("-profile test") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_references_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..bb700464 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,14 @@ +/* +======================================================================================== + Nextflow config file for running nf-test tests +======================================================================================== +*/ + +// TODO nf-core: Specify any additional parameters here +// Or any resources requirements +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/references' +} + +aws.client.anonymous = true // fixes S3 access issues on self-hosted runners From dddbfb4522c91bae5943d11f8523d7cef0b924cb Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 16 Oct 2025 13:38:52 +0000 Subject: [PATCH 05/25] Template update for nf-core/tools version 3.4.1 --- .devcontainer/devcontainer.json | 28 ++++---- .devcontainer/setup.sh | 13 ++++ .github/PULL_REQUEST_TEMPLATE.md | 4 +- .github/actions/nf-test/action.yml | 6 +- .github/workflows/awsfulltest.yml | 12 ++-- .github/workflows/awstest.yml | 12 ++-- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 6 +- .github/workflows/fix_linting.yml | 16 ++--- .github/workflows/linting.yml | 14 ++-- .github/workflows/linting_comment.yml | 2 +- .github/workflows/nf-test.yml | 9 +-- .github/workflows/release-announcements.yml | 7 ++ .../workflows/template-version-comment.yml | 2 +- .gitpod.yml | 10 --- .nf-core.yml | 5 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + CHANGELOG.md | 2 +- README.md | 5 +- assets/multiqc_config.yml | 4 +- assets/schema_input.json | 2 +- docs/usage.md | 2 +- main.nf | 5 +- modules.json | 8 +-- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 18 ++--- modules/nf-core/multiqc/tests/tags.yml | 2 - nextflow.config | 67 ++++++------------- nextflow_schema.json | 14 +++- ro-crate-metadata.json | 51 +++++--------- .../utils_nfcore_references_pipeline/main.nf | 31 ++++++++- .../utils_nextflow_pipeline/tests/tags.yml | 2 - .../utils_nfcore_pipeline/tests/tags.yml | 2 - .../nf-core/utils_nfschema_plugin/main.nf | 40 +++++++++-- .../utils_nfschema_plugin/tests/main.nf.test | 56 ++++++++++++++++ .../tests/nextflow.config | 4 +- tests/.nftignore | 3 +- tests/default.nf.test | 2 - 40 files changed, 283 insertions(+), 194 deletions(-) create mode 100755 .devcontainer/setup.sh delete mode 100644 .gitpod.yml delete mode 100644 modules/nf-core/multiqc/tests/tags.yml delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index b290e090..97c8c97f 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,20 +1,20 @@ { "name": "nfcore", - "image": "nfcore/gitpod:latest", - "remoteUser": "gitpod", - "runArgs": ["--privileged"], + "image": "nfcore/devcontainer:latest", - // Configure tool-specific properties. - "customizations": { - // Configure properties specific to VS Code. - "vscode": { - // Set *default* container specific settings.json values on container create. - "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python" - }, + "remoteUser": "root", + "privileged": true, - // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } + "remoteEnv": { + // Workspace path on the host for mounting with docker-outside-of-docker + "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" + }, + + "onCreateCommand": "./.devcontainer/setup.sh", + + "hostRequirements": { + "cpus": 4, + "memory": "16gb", + "storage": "32gb" } } diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh new file mode 100755 index 00000000..12bfe425 --- /dev/null +++ b/.devcontainer/setup.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +# Customise the terminal command prompt +echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc +echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc +export PROMPT_DIRTRIM=2 +export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' + +# Update Nextflow +nextflow self-update + +# Update welcome message +echo "Welcome to the nf-core/references devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index b322ee95..034a6fc9 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/references/tree/master/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/references/tree/main/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/references/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/references/tree/main/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/references _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index bf44d961..3b9724c7 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -25,9 +25,9 @@ runs: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install nf-test uses: nf-core/setup-nf-test@v1 @@ -52,6 +52,8 @@ runs: with: auto-update-conda: true conda-solver: libmamba + channels: conda-forge + channel-priority: strict conda-remove-defaults: true - name: Run nf-test diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 2b1f3e60..e743314a 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -28,15 +28,15 @@ jobs: # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ steps.revision.outputs.revision }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/references/work-${{ steps.revision.outputs.revision }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/references/work-${{ steps.revision.outputs.revision }} parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/references/results-${{ steps.revision.outputs.revision }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/references/results-${{ steps.revision.outputs.revision }}" } profiles: test_full @@ -44,5 +44,5 @@ jobs: with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index e1b779ff..9d1d5e65 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -14,14 +14,14 @@ jobs: - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/references/work-${{ github.sha }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/references/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/references/results-test-${{ github.sha }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/references/results-test-${{ github.sha }}" } profiles: test @@ -29,5 +29,5 @@ jobs: with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index ac030fd5..6adb0fff 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9 + - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 999bcc38..6d94bcbf 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -44,9 +44,9 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" architecture: "x64" - name: Setup Apptainer @@ -57,7 +57,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git@dev + pip install git+https://github.com/nf-core/tools.git - name: Make a cache directory for the container images run: | diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 23e74651..753250e4 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,13 +13,13 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} # indication that the linting is being fixed - name: React on comment - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: eyes @@ -32,9 +32,9 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install pre-commit run: pip install pre-commit @@ -47,7 +47,7 @@ jobs: # indication that the linting has finished - name: react if linting finished succesfully if: steps.pre-commit.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: "+1" @@ -67,21 +67,21 @@ jobs: - name: react if linting errors were fixed id: react-if-fixed if: steps.commit-and-push.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: hooray - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: confused - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: issue-number: ${{ github.event.issue.number }} body: | diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8b0f88c3..30e66026 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,12 +11,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - - name: Set up Python 3.13 - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - name: Set up Python 3.14 + uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install pre-commit run: pip install pre-commit @@ -28,14 +28,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" architecture: "x64" - name: read .nf-core.yml diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index d43797d9..e6e9bc26 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2 + uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index e7b58449..e20bf6d0 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -18,7 +18,7 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.2" + NFT_VER: "0.9.3" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: fetch-depth: 0 @@ -78,14 +78,14 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "24.10.5" + - "25.04.0" - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: fetch-depth: 0 @@ -95,6 +95,7 @@ jobs: continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + NXF_VERSION: ${{ matrix.NXF_VER }} with: profile: ${{ matrix.profile }} shard: ${{ matrix.shard }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 0f732495..e64cebd6 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -14,6 +14,11 @@ jobs: run: | echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT + - name: get description + id: get_topics + run: | + echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -23,6 +28,8 @@ jobs: message: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + ${{ steps.get_topics.outputs.description }} + Please see the changelog: ${{ github.event.release.html_url }} ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index beb5c77f..c5988af9 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index 83599f63..00000000 --- a/.gitpod.yml +++ /dev/null @@ -1,10 +0,0 @@ -image: nfcore/gitpod:latest -tasks: - - name: Update Nextflow and setup pre-commit - command: | - pre-commit install --install-hooks - nextflow self-update - -vscode: - extensions: - - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index b31e7002..192bde39 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,7 +1,6 @@ lint: actions_awsfulltest: false files_exist: - - .github/workflows/ci.yml - conf/igenomes.config - conf/igenomes_ignored.config files_unchanged: @@ -10,7 +9,7 @@ lint: - assets/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_dark.png -nf_core_version: 3.3.2 +nf_core_version: 3.4.1 repository_type: pipeline template: author: "@maxulysse" @@ -23,4 +22,4 @@ template: skip_features: - fastqc - igenomes - version: 1.0dev + version: "0.2" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bb41beec..d06777a8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ repos: additional_dependencies: - prettier@3.6.2 - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 + rev: v6.0.0 hooks: - id: trailing-whitespace args: [--markdown-linebreak-ext=md] diff --git a/.prettierignore b/.prettierignore index edd29f01..2255e3e3 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,4 +10,5 @@ testing/ testing* *.pyc bin/ +.nf-test/ ro-crate-metadata.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 203d553b..17e806bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0dev - [date] +## v0.2 - [date] Initial release of nf-core/references, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 13e0006b..2068d10d 100644 --- a/README.md +++ b/README.md @@ -5,12 +5,13 @@ +[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/references) [![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 698e905c..4c9027b7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/references + This report has been generated by the nf-core/references analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-references-methods-description": order: -1000 diff --git a/assets/schema_input.json b/assets/schema_input.json index 98ff18f4..f1962202 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/references/master/assets/schema_input.json", + "$id": "https://raw.githubusercontent.com/nf-core/references/main/assets/schema_input.json", "title": "nf-core/references pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", diff --git a/docs/usage.md b/docs/usage.md index eb869899..9731efc2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -148,7 +148,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `shifter` - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) + - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` diff --git a/main.nf b/main.nf index 0a5037da..6a795ccd 100644 --- a/main.nf +++ b/main.nf @@ -61,7 +61,10 @@ workflow { params.monochrome_logs, args, params.outdir, - params.input + params.input, + params.help, + params.help_full, + params.show_hidden ) // diff --git a/modules.json b/modules.json index 62fb0a84..6b0d530a 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b", "installed_by": ["modules"] } } @@ -16,17 +16,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", + "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 812fc4c5..dd513cbd 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.29 + - bioconda::multiqc=1.31 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 0ac3c369..5288f5cc 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : - 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' : + 'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 88e90571..17881d15 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-22T11:50:41.182332996" + "timestamp": "2025-09-08T20:57:36.139055243" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-22T11:51:22.448739369" + "timestamp": "2025-09-08T20:59:15.142230631" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-22T11:51:06.198928424" + "timestamp": "2025-09-08T20:58:29.629087066" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d3..00000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index fe6b64b1..9e5df4eb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,13 +27,15 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = null + hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + + // Config options config_profile_name = null config_profile_description = null @@ -86,7 +88,18 @@ profiles { apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' } - arm { + arm64 { + process.arch = 'arm64' + // TODO https://github.com/nf-core/modules/issues/6694 + // For now if you're using arm64 you have to use wave for the sake of the maintainers + // wave profile + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + emulate_amd64 { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { @@ -143,18 +156,6 @@ profiles { wave.freeze = true wave.strategy = 'conda,container' } - gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB - process { - resourceLimits = [ - memory: 8.GB, - cpus : 4, - time : 1.h - ] - } - } gpu { docker.runOptions = '-u $(id -u):$(id -g) --gpus all' apptainer.runOptions = '--nv' @@ -163,7 +164,6 @@ profiles { test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } - // Load nf-core custom profiles from different institutions // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. @@ -243,47 +243,20 @@ manifest { homePage = 'https://github.com/nf-core/references' description = """help community build references""" mainScript = 'main.nf' - defaultBranch = 'master' - nextflowVersion = '!>=24.10.5' - version = '1.0dev' + defaultBranch = 'main' + nextflowVersion = '!>=25.04.0' + version = '0.2' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs - help { - enabled = true - command = "nextflow run nf-core/references -profile --input samplesheet.csv --outdir " - fullParameter = "help_full" - showHiddenParameter = "show_hidden" - beforeText = """ --\033[2m----------------------------------------------------\033[0m- - \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m -\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m -\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m -\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m - \033[0;32m`._,._,\'\033[0m -\033[0;35m nf-core/references ${manifest.version}\033[0m --\033[2m----------------------------------------------------\033[0m- -""" - afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} -* The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies - https://github.com/nf-core/references/blob/master/CITATIONS.md -""" - } - summary { - beforeText = validation.help.beforeText - afterText = validation.help.afterText - } } // Load modules.config for DSL2 module specific options diff --git a/nextflow_schema.json b/nextflow_schema.json index e4170b9f..11172776 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/references/master/nextflow_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/references/main/nextflow_schema.json", "title": "nf-core/references pipeline parameters", "description": "help community build references", "type": "object", @@ -185,6 +185,18 @@ "fa_icon": "far calendar", "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", "hidden": true + }, + "help": { + "type": ["boolean", "string"], + "description": "Display the help message." + }, + "help_full": { + "type": "boolean", + "description": "Display the full detailed help message." + }, + "show_hidden": { + "type": "boolean", + "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)." } } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index dea54367..41865af8 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2025-07-14T09:36:06+00:00", - "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "creativeWorkStatus": "Stable", + "datePublished": "2025-10-16T13:38:48+00:00", + "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#7013769a-0bdc-4319-8311-26037f814cf4" + "@id": "#ecb10fa2-716f-4257-b106-a76fa36efb02" } ], "name": "nf-core/references" @@ -121,40 +121,21 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-07-14T11:36:06Z", + "dateModified": "2025-10-16T13:38:48Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", - "keywords": [ - "nf-core", - "nextflow", - "genome", - "references", - "reproducibility" - ], - "license": [ - "MIT" - ], - "name": [ - "nf-core/references" - ], + "keywords": ["nf-core", "nextflow", "genome", "references", "reproducibility"], + "license": ["MIT"], + "name": ["nf-core/references"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/nf-core/references", - "https://nf-co.re/references/dev/" - ], - "version": [ - "1.0dev" - ] + "url": ["https://github.com/nf-core/references", "https://nf-co.re/references/0.2/"], + "version": ["0.2"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -166,14 +147,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.10.5" + "version": "!>=25.04.0" }, { - "@id": "#7013769a-0bdc-4319-8311-26037f814cf4", + "@id": "#ecb10fa2-716f-4257-b106-a76fa36efb02", "@type": "TestSuite", "instance": [ { - "@id": "#68c4672c-6c98-4bb0-bc81-e5cd34d66762" + "@id": "#9fec957d-a657-4e19-9839-941f7e4ac8d1" } ], "mainEntity": { @@ -182,7 +163,7 @@ "name": "Test suite for nf-core/references" }, { - "@id": "#68c4672c-6c98-4bb0-bc81-e5cd34d66762", + "@id": "#9fec957d-a657-4e19-9839-941f7e4ac8d1", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/references", "resource": "repos/nf-core/references/actions/workflows/nf-test.yml", @@ -311,4 +292,4 @@ "url": "https://nf-co.re/" } ] -} \ No newline at end of file +} diff --git a/subworkflows/local/utils_nfcore_references_pipeline/main.nf b/subworkflows/local/utils_nfcore_references_pipeline/main.nf index 378a230f..59c01b94 100644 --- a/subworkflows/local/utils_nfcore_references_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_references_pipeline/main.nf @@ -11,6 +11,7 @@ include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' include { samplesheetToList } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' @@ -32,6 +33,9 @@ workflow PIPELINE_INITIALISATION { nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet + help // boolean: Display help message and exit + help_full // boolean: Show the full help message + show_hidden // boolean: Show hidden parameters in the help message main: @@ -50,10 +54,35 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // + before_text = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m nf-core/references ${workflow.manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/references/blob/main/CITATIONS.md +""" + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFSCHEMA_PLUGIN ( workflow, validate_params, - null + null, + help, + help_full, + show_hidden, + before_text, + after_text, + command ) // diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f8476112..00000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c9..00000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 4994303e..ee4738c8 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -4,6 +4,7 @@ include { paramsSummaryLog } from 'plugin/nf-schema' include { validateParameters } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' workflow UTILS_NFSCHEMA_PLUGIN { @@ -15,29 +16,56 @@ workflow UTILS_NFSCHEMA_PLUGIN { // when this input is empty it will automatically use the configured schema or // "${projectDir}/nextflow_schema.json" as default. This input should not be empty // for meta pipelines + help // boolean: show help message + help_full // boolean: show full help message + show_hidden // boolean: show hidden parameters in help message + before_text // string: text to show before the help message and parameters summary + after_text // string: text to show after the help message and parameters summary + command // string: an example command of the pipeline main: + if(help || help_full) { + help_options = [ + beforeText: before_text, + afterText: after_text, + command: command, + showHidden: show_hidden, + fullHelp: help_full, + ] + if(parameters_schema) { + help_options << [parametersSchema: parameters_schema] + } + log.info paramsHelp( + help_options, + params.help instanceof String ? params.help : "", + ) + exit 0 + } + // // Print parameter summary to stdout. This will display the parameters // that differ from the default given in the JSON schema // + + summary_options = [:] if(parameters_schema) { - log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) - } else { - log.info paramsSummaryLog(input_workflow) + summary_options << [parametersSchema: parameters_schema] } + log.info before_text + log.info paramsSummaryLog(summary_options, input_workflow) + log.info after_text // // Validate the parameters using nextflow_schema.json or the schema // given via the validation.parametersSchema configuration option // if(validate_params) { + validateOptions = [:] if(parameters_schema) { - validateParameters(parameters_schema:parameters_schema) - } else { - validateParameters() + validateOptions << [parametersSchema: parameters_schema] } + validateParameters(validateOptions) } emit: diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 8fb30164..c977917a 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -25,6 +25,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -51,6 +57,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -77,6 +89,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -103,6 +121,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -114,4 +138,36 @@ nextflow_workflow { ) } } + + test("Should create a help message") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = true + input[4] = false + input[5] = false + input[6] = "Before" + input[7] = "After" + input[8] = "nextflow run test/test" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 09ef842a..8d8c7371 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,8 +1,8 @@ plugins { - id "nf-schema@2.4.2" + id "nf-schema@2.5.1" } validation { parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" monochromeLogs = true -} \ No newline at end of file +} diff --git a/tests/.nftignore b/tests/.nftignore index 16409f40..83f7a0a5 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,9 +1,10 @@ .DS_Store -multiqc/multiqc_data/BETA-multiqc.parquet +multiqc/multiqc_data/multiqc.parquet multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_data/llms-full.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html pipeline_info/*.{html,json,txt,yml} diff --git a/tests/default.nf.test b/tests/default.nf.test index 8a2e92c9..4a7eb769 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -20,8 +20,6 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_references_software_mqc_versions.yml"), // All stable path name, with a relative path From 0256a0a7cced6e28f76a9e69794889089bbde402 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 20 Nov 2025 09:32:26 +0000 Subject: [PATCH 06/25] Template update for nf-core/tools version 3.5.1 --- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/download_pipeline.yml | 2 +- .github/workflows/fix_linting.yml | 2 +- .github/workflows/linting.yml | 6 +-- .github/workflows/nf-test.yml | 4 +- .github/workflows/release-announcements.yml | 9 ++--- .../workflows/template-version-comment.yml | 2 +- .nf-core.yml | 2 +- .prettierignore | 2 + README.md | 4 +- modules.json | 4 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 24 ++++++------ nextflow.config | 1 + ro-crate-metadata.json | 14 +++---- .../utils_nfcore_references_pipeline/main.nf | 6 +-- .../nf-core/utils_nfcore_pipeline/main.nf | 2 +- workflows/references.nf | 38 ++++++++++++++----- 20 files changed, 75 insertions(+), 57 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index e743314a..f6366711 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -40,7 +40,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 9d1d5e65..18f73be8 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 6d94bcbf..45884ff9 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -127,7 +127,7 @@ jobs: fi - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: nextflow_logfile.txt path: .nextflow.log* diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 753250e4..6c8fcc16 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 30e66026..7a527a34 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,7 +11,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - name: Set up Python 3.14 uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -71,7 +71,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: linting-logs path: | diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index e20bf6d0..c98d76ec 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: fetch-depth: 0 @@ -85,7 +85,7 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: fetch-depth: 0 diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index e64cebd6..431d3d44 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -15,10 +15,9 @@ jobs: echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - name: get description - id: get_topics + id: get_description run: | - echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT - + echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -27,9 +26,7 @@ jobs: # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release message: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - ${{ steps.get_topics.outputs.description }} - + ${{ steps.get_description.outputs.description }} Please see the changelog: ${{ github.event.release.html_url }} ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index c5988af9..e8560fc7 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.nf-core.yml b/.nf-core.yml index 192bde39..ed2fd060 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,7 +9,7 @@ lint: - assets/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_dark.png -nf_core_version: 3.4.1 +nf_core_version: 3.5.1 repository_type: pipeline template: author: "@maxulysse" diff --git a/.prettierignore b/.prettierignore index 2255e3e3..dd749d43 100644 --- a/.prettierignore +++ b/.prettierignore @@ -12,3 +12,5 @@ testing* bin/ .nf-test/ ro-crate-metadata.json +modules/nf-core/ +subworkflows/nf-core/ diff --git a/README.md b/README.md index 2068d10d..44988ab5 100644 --- a/README.md +++ b/README.md @@ -5,13 +5,13 @@ -[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/references) +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/references) [![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/modules.json b/modules.json index 6b0d530a..674fb04e 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b", + "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", "installed_by": ["modules"] } } @@ -21,7 +21,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index dd513cbd..d02016a0 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.31 + - bioconda::multiqc=1.32 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 5288f5cc..c1158fb0 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' : - 'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' : + 'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 17881d15..a88bafd6 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "24.10.4" }, - "timestamp": "2025-09-08T20:57:36.139055243" + "timestamp": "2025-10-27T13:33:24.356715" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "24.10.4" }, - "timestamp": "2025-09-08T20:59:15.142230631" + "timestamp": "2025-10-27T13:34:11.103619" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "24.10.4" }, - "timestamp": "2025-09-08T20:58:29.629087066" + "timestamp": "2025-10-27T13:34:04.615233" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 9e5df4eb..1eae8876 100644 --- a/nextflow.config +++ b/nextflow.config @@ -164,6 +164,7 @@ profiles { test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } + // Load nf-core custom profiles from different institutions // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 41865af8..d1c235b2 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2025-10-16T13:38:48+00:00", - "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-11-20T09:32:21+00:00", + "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#ecb10fa2-716f-4257-b106-a76fa36efb02" + "@id": "#8c4f9188-ed0f-447e-8c1c-32236ef06865" } ], "name": "nf-core/references" @@ -123,7 +123,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-10-16T13:38:48Z", + "dateModified": "2025-11-20T09:32:21Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": ["nf-core", "nextflow", "genome", "references", "reproducibility"], "license": ["MIT"], @@ -150,11 +150,11 @@ "version": "!>=25.04.0" }, { - "@id": "#ecb10fa2-716f-4257-b106-a76fa36efb02", + "@id": "#8c4f9188-ed0f-447e-8c1c-32236ef06865", "@type": "TestSuite", "instance": [ { - "@id": "#9fec957d-a657-4e19-9839-941f7e4ac8d1" + "@id": "#b8032b85-6776-4fd2-9007-7f7a0e36b605" } ], "mainEntity": { @@ -163,7 +163,7 @@ "name": "Test suite for nf-core/references" }, { - "@id": "#9fec957d-a657-4e19-9839-941f7e4ac8d1", + "@id": "#b8032b85-6776-4fd2-9007-7f7a0e36b605", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/references", "resource": "repos/nf-core/references/actions/workflows/nf-test.yml", diff --git a/subworkflows/local/utils_nfcore_references_pipeline/main.nf b/subworkflows/local/utils_nfcore_references_pipeline/main.nf index 59c01b94..4a3fe6a7 100644 --- a/subworkflows/local/utils_nfcore_references_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_references_pipeline/main.nf @@ -39,7 +39,7 @@ workflow PIPELINE_INITIALISATION { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Print version and exit if required and dump pipeline parameters to JSON file @@ -64,7 +64,7 @@ workflow PIPELINE_INITIALISATION { \033[0;35m nf-core/references ${workflow.manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} + after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> " https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x @@ -96,7 +96,7 @@ workflow PIPELINE_INITIALISATION { // Create channel from input file provided through params.input // - Channel + channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index bfd25876..2f30e9a4 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -98,7 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML())) } // diff --git a/workflows/references.nf b/workflows/references.nf index 1abafc63..5b1b1da8 100644 --- a/workflows/references.nf +++ b/workflows/references.nf @@ -21,13 +21,31 @@ workflow REFERENCES { ch_samplesheet // channel: samplesheet read in from --input main: - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() + ch_versions = channel.empty() + ch_multiqc_files = channel.empty() // // Collate and save software versions // - softwareVersionsToYAML(ch_versions) + def topic_versions = Channel.topic("versions") + .distinct() + .branch { entry -> + versions_file: entry instanceof Path + versions_tuple: true + } + + def topic_versions_string = topic_versions.versions_tuple + .map { process, tool, version -> + [ process[process.lastIndexOf(':')+1..-1], " ${tool}: ${version}" ] + } + .groupTuple(by:0) + .map { process, tool_versions -> + tool_versions.unique().sort() + "${process}:\n${tool_versions.join('\n')}" + } + + softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + .mix(topic_versions_string) .collectFile( storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_' + 'references_software_' + 'mqc_' + 'versions.yml', @@ -39,24 +57,24 @@ workflow REFERENCES { // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath( + ch_multiqc_config = channel.fromPath( "$projectDir/assets/multiqc_config.yml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() + channel.fromPath(params.multiqc_config, checkIfExists: true) : + channel.empty() ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() + channel.fromPath(params.multiqc_logo, checkIfExists: true) : + channel.empty() summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value( + ch_methods_description = channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) From 8bdee1e1921c282b0a8c582bb2e9f0544cf28097 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 28 Apr 2026 11:20:59 +0000 Subject: [PATCH 07/25] Template update for nf-core/tools version 4.0.0 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 125 -- .github/PULL_REQUEST_TEMPLATE.md | 4 +- .github/actions/get-shards/action.yml | 2 +- .github/actions/nf-test/action.yml | 10 +- .github/workflows/awsfulltest.yml | 25 +- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 14 +- .github/workflows/fix_linting.yml | 22 +- .github/workflows/linting.yml | 34 +- .github/workflows/linting_comment.yml | 4 +- .github/workflows/nf-test.yml | 8 +- .github/workflows/release-announcements.yml | 4 +- .../workflows/template-version-comment.yml | 6 +- .gitignore | 1 + .nf-core.yml | 2 +- .pre-commit-config.yaml | 16 +- .prettierignore | 2 - README.md | 12 +- assets/adaptivecard.json | 67 - assets/slackreport.json | 34 - conf/base.config | 2 +- conf/containers_conda_lock_files_amd64.config | 1 + conf/containers_conda_lock_files_arm64.config | 1 + conf/containers_docker_amd64.config | 1 + conf/containers_docker_arm64.config | 1 + .../containers_singularity_https_amd64.config | 1 + .../containers_singularity_https_arm64.config | 1 + conf/containers_singularity_oras_amd64.config | 1 + conf/containers_singularity_oras_arm64.config | 1 + docs/CONTRIBUTING.md | 185 ++ docs/usage.md | 8 +- main.nf | 7 +- modules.json | 6 +- .../linux_amd64-bd-c1f4a7982b743963_1.txt | 1552 +++++++++++++++++ .../linux_amd64-bd-db7c73dae76bc9e6_1.txt | 126 ++ .../linux_arm64-bd-40bf3b435e89dc22_1.txt | 1502 ++++++++++++++++ .../linux_arm64-bd-d167b8012595a136_1.txt | 125 ++ modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 51 +- modules/nf-core/multiqc/meta.yml | 165 +- .../multiqc/tests/custom_prefix.config | 5 + modules/nf-core/multiqc/tests/main.nf.test | 191 +- .../nf-core/multiqc/tests/main.nf.test.snap | 435 ++++- modules/nf-core/multiqc/tests/nextflow.config | 1 + nextflow.config | 8 +- nextflow_schema.json | 7 - nf-test.config | 26 +- ro-crate-metadata.json | 30 +- .../utils_nfcore_references_pipeline/main.nf | 17 +- .../nf-core/utils_nfcore_pipeline/main.nf | 66 +- .../utils_nfcore_pipeline/tests/main.nf.test | 29 + .../tests/main.nf.test.snap | 19 + .../nf-core/utils_nfschema_plugin/main.nf | 3 +- .../tests/nextflow.config | 2 +- tests/default.nf.test | 14 +- tests/nextflow.config | 2 +- workflows/references.nf | 77 +- 60 files changed, 4449 insertions(+), 623 deletions(-) delete mode 100644 .github/CONTRIBUTING.md delete mode 100644 assets/adaptivecard.json delete mode 100644 assets/slackreport.json create mode 100644 conf/containers_conda_lock_files_amd64.config create mode 100644 conf/containers_conda_lock_files_arm64.config create mode 100644 conf/containers_docker_amd64.config create mode 100644 conf/containers_docker_arm64.config create mode 100644 conf/containers_singularity_https_amd64.config create mode 100644 conf/containers_singularity_https_arm64.config create mode 100644 conf/containers_singularity_oras_amd64.config create mode 100644 conf/containers_singularity_oras_arm64.config create mode 100644 docs/CONTRIBUTING.md create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt create mode 100644 modules/nf-core/multiqc/tests/custom_prefix.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 97c8c97f..237c9ed0 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,4 +1,5 @@ { + "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json", "name": "nfcore", "image": "nfcore/devcontainer:latest", diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 358d2650..00000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,125 +0,0 @@ -# `nf-core/references`: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/references. - -We try to manage the required tasks for nf-core/references using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -> [!NOTE] -> If you need help using or modifying nf-core/references then the best place to ask is on the nf-core Slack [#references](https://nfcore.slack.com/channels/references) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Contribution workflow - -If you'd like to write some code for nf-core/references, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/references issues](https://github.com/nf-core/references/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/references repository](https://github.com/nf-core/references) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: - -```bash -nf-test test --profile debug,test,docker --verbose -``` - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- Open a pull-request from `patch` to `main`/`master` with the changes. - -## Getting help - -For further information/help, please consult the [nf-core/references documentation](https://nf-co.re/references/usage) and don't hesitate to get in touch on the nf-core Slack [#references](https://nfcore.slack.com/channels/references) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the `nf-core/references` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test in the `tests` directory. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. - -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-core/references/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 034a6fc9..ca8b406f 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/references/tree/main/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/references/tree/main/docs/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/references/tree/main/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/references/tree/main/docs/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/references _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml index 34085279..e2833ee9 100644 --- a/.github/actions/get-shards/action.yml +++ b/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: ${{ env.NFT_VER }} - name: Get number of shards diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 3b9724c7..ad686e8e 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,24 +20,24 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: "${{ env.NFT_VER }}" install-pdiff: true - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@main + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2 - name: Set up Singularity if: contains(inputs.profile, 'singularity') @@ -48,7 +48,7 @@ runs: - name: Conda setup if: contains(inputs.profile, 'conda') - uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3 + uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 with: auto-update-conda: true conda-solver: libmamba diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index f6366711..5c83e2c1 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -23,7 +23,7 @@ jobs: echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -33,14 +33,33 @@ jobs: compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ steps.revision.outputs.revision }} workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/references/work-${{ steps.revision.outputs.revision }} + nextflow_config: | + plugins { + id 'nf-slack@0.5.0' + } + slack { + enabled = true + bot { + token = '${{ secrets.NFSLACK_BOT_TOKEN }}' + channel = 'references' + } + onStart { + enabled = false + } + onComplete { + message = ':white_check_mark: *references/test_full* completed successfully! :tada:' + } + onError { + message = ':x: *references/test_full* failed :crying_cat_face:' + } + } parameters: | { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/references/results-${{ steps.revision.outputs.revision }}" } profiles: test_full - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 18f73be8..fa15547e 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Seqera Platform CLI tool action - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 705a8ecb..9451d06f 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -21,7 +21,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 with: message: | ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 6adb0fff..172de6f3 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 + - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 45884ff9..5b6592c1 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -39,12 +39,12 @@ jobs: needs: configure steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" @@ -54,10 +54,16 @@ jobs: with: apptainer-version: 1.3.4 + - name: Read .nf-core.yml + uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Make a cache directory for the container images run: | @@ -127,7 +133,7 @@ jobs: fi - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: nextflow_logfile.txt path: .nextflow.log* diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 6c8fcc16..81f66927 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -31,22 +31,18 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - # Install and run pre-commit - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - id: pre-commit - run: pre-commit run --all-files + # Install and run prek + - name: Run prek + id: prek + uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 continue-on-error: true # indication that the linting has finished - name: react if linting finished succesfully - if: steps.pre-commit.outcome == 'success' + if: steps.prek.outcome == 'success' uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} @@ -54,7 +50,7 @@ jobs: - name: Commit & push changes id: commit-and-push - if: steps.pre-commit.outcome == 'failure' + if: steps.prek.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 7a527a34..bfe46c98 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,33 +11,31 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - - name: Set up Python 3.14 - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - run: pre-commit run --all-files + - name: Run prek + uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" + - name: Setup uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml @@ -45,12 +43,10 @@ jobs: config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' }} + if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -58,7 +54,7 @@ jobs: run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Run nf-core pipelines lint --release - if: ${{ github.base_ref == 'master' }} + if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -71,7 +67,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index e6e9bc26..2bc3c07f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 + uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 + uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c98d76ec..efd72d65 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -18,7 +18,7 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.3" + NFT_VER: "0.9.4" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 @@ -78,14 +78,14 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "25.04.0" + - "25.10.4" - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 431d3d44..78d5dbe0 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -18,7 +18,7 @@ jobs: id: get_description run: | echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT - - uses: rzr/fediverse-action@master + - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} host: "mstdn.science" # custom host if not "mastodon.social" (default) @@ -34,7 +34,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 + - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index e8560fc7..ea30827e 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: ref: ${{ github.event.pull_request.head.sha }} @@ -29,7 +29,7 @@ jobs: run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 if: | contains(env.OUTPUT, 'nf-core') with: @@ -42,5 +42,5 @@ jobs: > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. > Please update your pipeline to the latest version. > - > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). # diff --git a/.gitignore b/.gitignore index a42ce016..cc2b1a77 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ testing/ testing* *.pyc null/ +.lineage/ diff --git a/.nf-core.yml b/.nf-core.yml index ed2fd060..28312266 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,7 +9,7 @@ lint: - assets/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_dark.png -nf_core_version: 3.5.1 +nf_core_version: 4.0.0 repository_type: pipeline template: author: "@maxulysse" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d06777a8..f51e1a28 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.6.2 + - prettier@3.8.3 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -13,15 +13,21 @@ repos: exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ - id: end-of-file-fixer exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.3.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' + args: ["-output", "json"] diff --git a/.prettierignore b/.prettierignore index dd749d43..63cde500 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,6 +1,4 @@ email_template.html -adaptivecard.json -slackreport.json .nextflow* work/ data/ diff --git a/README.md b/README.md index 44988ab5..5f020360 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -30,13 +30,13 @@ --> + workflows use the "tube map" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples. --> 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data. diff --git a/docs/usage.md b/docs/usage.md index 9731efc2..96a47d2f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -76,7 +76,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > [!WARNING] -> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -172,19 +172,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. +To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website. ### Custom Containers In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. -To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website. ### Custom Tool Arguments A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/main.nf b/main.nf index 6a795ccd..b69070c2 100644 --- a/main.nf +++ b/main.nf @@ -38,7 +38,11 @@ workflow NFCORE_REFERENCES { // WORKFLOW: Run pipeline // REFERENCES ( - samplesheet + samplesheet, + params.multiqc_config, + params.multiqc_logo, + params.multiqc_methods_description, + params.outdir, ) emit: multiqc_report = REFERENCES.out.multiqc_report // channel: /path/to/multiqc_report.html @@ -82,7 +86,6 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - params.hook_url, NFCORE_REFERENCES.out.multiqc_report ) } diff --git a/modules.json b/modules.json index 674fb04e..36e61dbd 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", + "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", + "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", + "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", "installed_by": ["subworkflows"] } } diff --git 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b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.32 + - bioconda::multiqc=1.34 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index c1158fb0..e80e8cd8 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,24 +1,21 @@ process MULTIQC { + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' : - 'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' + : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - path(replace_names) - path(sample_names) + tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions + tuple val(meta), path("*.html"), emit: report + tuple val(meta), path("*_data"), emit: data + tuple val(meta), path("*_plots"), emit: plots, optional: true + // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever + tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions when: task.ext.when == null || task.ext.when @@ -26,38 +23,28 @@ process MULTIQC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : "" def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' def replace = replace_names ? "--replace-names ${replace_names}" : '' def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ - $args \\ - $config \\ - $prefix \\ - $extra_config \\ - $logo \\ - $replace \\ - $samples \\ + ${args} \\ + ${config} \\ + ${prefix} \\ + ${logo} \\ + ${replace} \\ + ${samples} \\ . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ stub: """ mkdir multiqc_data + touch multiqc_data/.stub mkdir multiqc_plots + touch multiqc_plots/.stub touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ce30eb73..2facc627 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,6 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into - a single report +description: Aggregate results from bioinformatics analyses across many samples + into a single report keywords: - QC - bioinformatics tools @@ -12,74 +12,91 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - ontologies: [] - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - ontologies: [] - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV -output: - report: - - "*multiqc_report.html": + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - multiqc_files: type: file - description: MultiQC report file - pattern: "multiqc_report.html" + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC ontologies: [] - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - plots: - - "*_plots": + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 + - multiqc_logo: type: file - description: Plots created by MultiQC - pattern: "*_data" + description: Optional logo file for MultiQC + pattern: "*.{png}" ontologies: [] - versions: - - versions.yml: + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 + - sample_names: type: file - description: File containing software versions - pattern: "versions.yml" + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - edam: http://edamontology.org/format_3475 +output: + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*.html": + type: file + description: MultiQC report file + pattern: ".html" + ontologies: [] + data: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_plots" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g": + type: eval + description: The expression to obtain the version of the tool authors: - "@abhi18av" - "@bunop" @@ -90,3 +107,27 @@ maintainers: - "@bunop" - "@drpatelh" - "@jfy133" +containers: + conda: + linux/amd64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + linux/arm64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt + docker: + linux/amd64: + name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 + build_id: bd-db7c73dae76bc9e6_1 + scan_id: sc-66fc7138dbf1cf48_1 + linux/arm64: + name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 + build_id: bd-d167b8012595a136_1 + scan_id: sc-ac701dfa631a2af9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 + build_id: bd-4fc8657c816047c0_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + linux/arm64: + name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 + build_id: bd-7fbd82d945c06726_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config new file mode 100644 index 00000000..b30b1358 --- /dev/null +++ b/modules/nf-core/multiqc/tests/custom_prefix.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = "custom_prefix" + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7d..4cbdb95d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -15,25 +15,84 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] - custom prefix") { + config "./custom_prefix.config" + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) + """ + } } + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } } test("sarscov2 single-end [fastqc] [config]") { @@ -41,23 +100,85 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] [multiple configs]") { + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [ + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true) + ], + [], + [], + [] + ]) + """ + } + } + + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -68,25 +189,23 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index a88bafd6..7c2f370f 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,41 +1,422 @@ { - "multiqc_versions_single": { + "sarscov2 single-end [fastqc] [multiple configs]": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } ], + "timestamp": "2026-03-17T16:15:42.577775492", "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" - }, - "timestamp": "2025-10-27T13:33:24.356715" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_stub": { + "sarscov2 single-end [fastqc]": { "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } ], + "timestamp": "2026-03-17T16:21:17.072841555", "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" - }, - "timestamp": "2025-10-27T13:34:11.103619" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_versions_config": { + "sarscov2 single-end [fastqc] - stub": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "data": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "plots": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "report": [ + [ + { + "id": "FASTQC" + }, + "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } ], + "timestamp": "2026-02-26T15:14:39.789193051", "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" - }, - "timestamp": "2025-10-27T13:34:04.615233" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] [config]": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:30.372239611", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] - 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hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false @@ -48,6 +47,10 @@ params { validate_params = true } +// Backwards compatibility for publishDir syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -245,7 +248,7 @@ manifest { description = """help community build references""" mainScript = 'main.nf' defaultBranch = 'main' - nextflowVersion = '!>=25.04.0' + nextflowVersion = '!>=25.10.4' version = '0.2' doi = '' } @@ -259,6 +262,5 @@ validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs } - // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 11172776..0b430fd9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -141,13 +141,6 @@ "fa_icon": "fas fa-palette", "hidden": true }, - "hook_url": { - "type": "string", - "description": "Incoming hook URL for messaging service", - "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", - "hidden": true - }, "multiqc_config": { "type": "string", "format": "file-path", diff --git a/nf-test.config b/nf-test.config index 3a1fff59..f7aaeb4a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,21 +1,35 @@ config { // location for all nf-test tests - testsDir "." + testsDir = "." // nf-test directory including temporary files for each test - workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests - configFile "tests/nextflow.config" + configFile = "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' + ignore = [ + 'modules/nf-core/**/tests/*', + 'subworkflows/nf-core/**/tests/*', + ] // run all test with defined profile(s) from the main nextflow.config - profile "test" + profile = "test" // list of filenames or patterns that should be trigger a full test run - triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' + triggers = [ + '.github/actions/nf-test/action.yml', + '.github/workflows/nf-test.yml', + 'assets/schema_input.json', + 'bin/*', + 'conf/test.config', + 'nextflow.config', + 'nextflow_schema.json', + 'nf-test.config', + 'tests/.nftignore', + 'tests/nextflow.config', + ] // load the necessary plugins plugins { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d1c235b2..05dcb369 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -1,6 +1,6 @@ { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", { "GithubService": "https://w3id.org/ro/terms/test#GithubService", "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2025-11-20T09:32:21+00:00", - "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-04-28T11:20:51+00:00", + "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#8c4f9188-ed0f-447e-8c1c-32236ef06865" + "@id": "#8b6aaf4f-c825-459d-b991-53bab2b7df6c" } ], "name": "nf-core/references" @@ -112,7 +112,7 @@ }, "conformsTo": [ { - "@id": "https://w3id.org/ro/crate/1.1" + "@id": "https://w3id.org/ro/crate/1.2" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -122,8 +122,13 @@ { "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "contributor": [ + { + "@id": "#78aa7a93-02e1-4cac-9a01-463f32234f7e" + } + ], "dateCreated": "", - "dateModified": "2025-11-20T09:32:21Z", + "dateModified": "2026-04-28T11:20:51Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": ["nf-core", "nextflow", "genome", "references", "reproducibility"], "license": ["MIT"], @@ -147,14 +152,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=25.04.0" + "version": "!>=25.10.4" }, { - "@id": "#8c4f9188-ed0f-447e-8c1c-32236ef06865", + "@id": "#8b6aaf4f-c825-459d-b991-53bab2b7df6c", "@type": "TestSuite", "instance": [ { - "@id": "#b8032b85-6776-4fd2-9007-7f7a0e36b605" + "@id": "#d9e22e83-5272-42fa-9a25-63b9ecce3756" } ], "mainEntity": { @@ -163,7 +168,7 @@ "name": "Test suite for nf-core/references" }, { - "@id": "#b8032b85-6776-4fd2-9007-7f7a0e36b605", + "@id": "#d9e22e83-5272-42fa-9a25-63b9ecce3756", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/references", "resource": "repos/nf-core/references/actions/workflows/nf-test.yml", @@ -290,6 +295,11 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" + }, + { + "@id": "#78aa7a93-02e1-4cac-9a01-463f32234f7e", + "@type": "Person", + "name": "@maxulysse" } ] } diff --git a/subworkflows/local/utils_nfcore_references_pipeline/main.nf b/subworkflows/local/utils_nfcore_references_pipeline/main.nf index 4a3fe6a7..e6f2fe07 100644 --- a/subworkflows/local/utils_nfcore_references_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_references_pipeline/main.nf @@ -14,7 +14,6 @@ include { samplesheetToList } from 'plugin/nf-schema' include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' @@ -54,6 +53,9 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // + + def before_text = "" + def after_text = "" before_text = """ -\033[2m----------------------------------------------------\033[0m- \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m @@ -71,6 +73,10 @@ workflow PIPELINE_INITIALISATION { * Software dependencies https://github.com/nf-core/references/blob/main/CITATIONS.md """ + if (monochrome_logs) { + before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '') + } + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " UTILS_NFSCHEMA_PLUGIN ( @@ -97,7 +103,7 @@ workflow PIPELINE_INITIALISATION { // channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -135,7 +141,6 @@ workflow PIPELINE_COMPLETION { plaintext_email // boolean: Send plain-text email instead of HTML outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: @@ -159,13 +164,11 @@ workflow PIPELINE_COMPLETION { } completionSummary(monochrome_logs) - if (hook_url) { - imNotification(summary_params, hook_url) - } + } workflow.onError { - log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting" } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 2f30e9a4..afca5439 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE { checkProfileProvided(nextflow_cli_args) emit: - valid_config + valid_config = valid_config } /* @@ -353,67 +353,3 @@ def completionSummary(monochrome_logs=true) { log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } - -// -// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack -// -def imNotification(summary_params, hook_url) { - def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) { - misc_fields['repository'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['commitid'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['revision'] = workflow.revision - } - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = getWorkflowVersion() - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("${workflow.projectDir}/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection() - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")) - def postRC = post.getResponseCode() - if (!postRC.equals(200)) { - log.warn(post.getErrorStream().getText()) - } -} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap new file mode 100644 index 00000000..859d1030 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index ee4738c8..1df8b76f 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { } log.info paramsHelp( help_options, - params.help instanceof String ? params.help : "", + (params.help instanceof String && params.help != "true") ? params.help : "", ) exit 0 } @@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN { emit: dummy_emit = true } - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 8d8c7371..f6537cc3 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.5.1" + id "nf-schema@2.6.1" } validation { diff --git a/tests/default.nf.test b/tests/default.nf.test index 4a7eb769..513ec0b2 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -13,19 +13,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assert workflow.success assertAll( - { assert workflow.success}, { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_references_software_mqc_versions.yml"), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/nextflow.config b/tests/nextflow.config index bb700464..b63274ac 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -8,7 +8,7 @@ // Or any resources requirements params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/references' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/references/' } aws.client.anonymous = true // fixes S3 access issues on self-hosted runners diff --git a/workflows/references.nf b/workflows/references.nf index 5b1b1da8..e425e5e7 100644 --- a/workflows/references.nf +++ b/workflows/references.nf @@ -19,15 +19,20 @@ workflow REFERENCES { take: ch_samplesheet // channel: samplesheet read in from --input + multiqc_config + multiqc_logo + multiqc_methods_description + outdir + main: - ch_versions = channel.empty() - ch_multiqc_files = channel.empty() + def ch_versions = channel.empty() + def ch_multiqc_files = channel.empty() // // Collate and save software versions // - def topic_versions = Channel.topic("versions") + def topic_versions = channel.topic("versions") .distinct() .branch { entry -> versions_file: entry instanceof Path @@ -44,59 +49,43 @@ workflow REFERENCES { "${process}:\n${tool_versions.join('\n')}" } - softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) .mix(topic_versions_string) .collectFile( - storeDir: "${params.outdir}/pipeline_info", + storeDir: "${outdir}/pipeline_info", name: 'nf_core_' + 'references_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true - ).set { ch_collated_versions } - + ) // // MODULE: MultiQC // - ch_multiqc_config = channel.fromPath( - "$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? - channel.fromPath(params.multiqc_config, checkIfExists: true) : - channel.empty() - ch_multiqc_logo = params.multiqc_logo ? - channel.fromPath(params.multiqc_logo, checkIfExists: true) : - channel.empty() - - summary_params = paramsSummaryMap( - workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? - file(params.multiqc_methods_description, checkIfExists: true) : - file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = channel.value( - methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix( - ch_methods_description.collectFile( - name: 'methods_description_mqc.yaml', - sort: true - ) - ) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), - [], - [] + def ch_summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def ch_workflow_summary = channel.value(paramsSummaryMultiqc(ch_summary_params)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + def ch_multiqc_custom_methods_description = multiqc_methods_description + ? file(multiqc_methods_description, checkIfExists: true) + : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true) + def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) + MULTIQC( + ch_multiqc_files.flatten().collect().map { files -> + [ + [id: 'references'], + files, + multiqc_config + ? file(multiqc_config, checkIfExists: true) + : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), + multiqc_logo ? file(multiqc_logo, checkIfExists: true) : [], + [], + [], + ] + } ) - - emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] - } /* From 29a5b2a1b49c3981f69edce4bafe84e77d2a0684 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 30 Apr 2026 07:37:02 +0000 Subject: [PATCH 08/25] Template update for nf-core/tools version 4.0.1 --- .github/workflows/fix_linting.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/linting_comment.yml | 2 +- .nf-core.yml | 2 +- README.md | 2 +- ro-crate-metadata.json | 18 +++++++++--------- 6 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 81f66927..0ec6677b 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -37,7 +37,7 @@ jobs: # Install and run prek - name: Run prek id: prek - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 continue-on-error: true # indication that the linting has finished diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bfe46c98..8738ffc9 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -17,7 +17,7 @@ jobs: uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - name: Run prek - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 nf-core: runs-on: ubuntu-latest diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 2bc3c07f..5b0c24f7 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20 + uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.nf-core.yml b/.nf-core.yml index 28312266..2e7bf6bf 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,7 +9,7 @@ lint: - assets/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_light.png - docs/images/nf-core-references_logo_dark.png -nf_core_version: 4.0.0 +nf_core_version: 4.0.1 repository_type: pipeline template: author: "@maxulysse" diff --git a/README.md b/README.md index 5f020360..31ed0d4c 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 05dcb369..15f7906f 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2026-04-28T11:20:51+00:00", - "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-04-30T07:36:54+00:00", + "description": "

    \n \n \n \"nf-core/references\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/references \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by @maxulysse.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#8b6aaf4f-c825-459d-b991-53bab2b7df6c" + "@id": "#35c27ac5-ba08-4fc5-8c56-0fc212432378" } ], "name": "nf-core/references" @@ -124,11 +124,11 @@ "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "contributor": [ { - "@id": "#78aa7a93-02e1-4cac-9a01-463f32234f7e" + "@id": "#acf498d1-a568-46fd-a16a-d61b2c70186b" } ], "dateCreated": "", - "dateModified": "2026-04-28T11:20:51Z", + "dateModified": "2026-04-30T07:36:54Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": ["nf-core", "nextflow", "genome", "references", "reproducibility"], "license": ["MIT"], @@ -155,11 +155,11 @@ "version": "!>=25.10.4" }, { - "@id": "#8b6aaf4f-c825-459d-b991-53bab2b7df6c", + "@id": "#35c27ac5-ba08-4fc5-8c56-0fc212432378", "@type": "TestSuite", "instance": [ { - "@id": "#d9e22e83-5272-42fa-9a25-63b9ecce3756" + "@id": "#dab1c7d4-bc70-4d03-b9f9-3547c29de632" } ], "mainEntity": { @@ -168,7 +168,7 @@ "name": "Test suite for nf-core/references" }, { - "@id": "#d9e22e83-5272-42fa-9a25-63b9ecce3756", + "@id": "#dab1c7d4-bc70-4d03-b9f9-3547c29de632", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/references", "resource": "repos/nf-core/references/actions/workflows/nf-test.yml", @@ -297,7 +297,7 @@ "url": "https://nf-co.re/" }, { - "@id": "#78aa7a93-02e1-4cac-9a01-463f32234f7e", + "@id": "#acf498d1-a568-46fd-a16a-d61b2c70186b", "@type": "Person", "name": "@maxulysse" } From cb816337679e61293049ea15e06bdba96d11fcb3 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Thu, 30 Apr 2026 10:37:33 +0200 Subject: [PATCH 09/25] prek --- .gitignore | 2 +- tests/.nftignore | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index bdc94005..e010de7a 100644 --- a/.gitignore +++ b/.gitignore @@ -13,4 +13,4 @@ null/ tmp/ .nf-test .vscode -modules/nf \ No newline at end of file +modules/nf diff --git a/tests/.nftignore b/tests/.nftignore index e8662666..479ada36 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -22,4 +22,4 @@ multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html -pipeline_info/*.{html,json,txt,yml} \ No newline at end of file +pipeline_info/*.{html,json,txt,yml} From d7d2dbdede54213726c37c8b12abefb9c0daac1d Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Thu, 30 Apr 2026 10:44:04 +0200 Subject: [PATCH 10/25] code polish --- tests/createsequencedictionary.nf.test | 6 +++--- tests/default.nf.test | 6 +++--- tests/hisat2.nf.test | 8 ++++---- tests/kallisto.nf.test | 8 ++++---- tests/multiple.nf.test | 4 ++-- tests/rsem.nf.test | 8 ++++---- tests/salmon.nf.test | 8 ++++---- tests/samtools.nf.test | 10 +++++----- tests/sarek.nf.test | 4 ++-- tests/tabix.nf.test | 4 ++-- tests/wbcel235.nf.test | 2 +- 11 files changed, 34 insertions(+), 34 deletions(-) diff --git a/tests/createsequencedictionary.nf.test b/tests/createsequencedictionary.nf.test index 3e0a1ef3..20e30d20 100644 --- a/tests/createsequencedictionary.nf.test +++ b/tests/createsequencedictionary.nf.test @@ -6,11 +6,11 @@ nextflow_pipeline { test("-profile test --tools createsequencedictionary") { - options "-output-dir $outputDir" + options "-output-dir ${outputDir}" when { params { - outdir = "$outputDir" + outdir = "${outputDir}" tools = 'createsequencedictionary' } } @@ -24,7 +24,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/default.nf.test b/tests/default.nf.test index a468371f..a44220c9 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -5,11 +5,11 @@ nextflow_pipeline { tag "pipeline" test("-profile test") { - options "-output-dir $outputDir" + options "-output-dir ${outputDir}" when { params { - outdir = "$outputDir" + outdir = "${outputDir}" } } @@ -22,7 +22,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_references_software_mqc_versions.yml"), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_path, // All files with stable contents diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 62e3d657..5d7cc0dd 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -28,7 +28,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -40,11 +40,11 @@ nextflow_pipeline { test("-profile test --tools hisat2,hisat2_extractsplicesites") { - options "-output-dir $outputDir" + options "-output-dir ${outputDir}" when { params { - outdir = "$outputDir" + outdir = "${outputDir}" tools = 'hisat2,hisat2_extractsplicesites' // TODO REMOVE ME when the module is fixed // cf https://github.com/nf-core/modules/issues/7045 @@ -61,7 +61,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index f49f1ae3..3afe67e7 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -37,11 +37,11 @@ nextflow_pipeline { test("-profile test --tools kallisto,rsem_make_transcript_fasta") { - options "-output-dir $outputDir" + options "-output-dir ${outputDir}" when { params { - outdir = "$outputDir" + outdir = "${outputDir}" tools = 'kallisto,rsem_make_transcript_fasta' } } @@ -55,7 +55,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/multiple.nf.test b/tests/multiple.nf.test index 15ef88c5..039080c7 100644 --- a/tests/multiple.nf.test +++ b/tests/multiple.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -56,7 +56,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/rsem.nf.test b/tests/rsem.nf.test index d877a445..1c12a804 100644 --- a/tests/rsem.nf.test +++ b/tests/rsem.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -37,11 +37,11 @@ nextflow_pipeline { test("-profile test --tools rsem,rsem_make_transcript_fasta") { - options "-output-dir $outputDir" + options "-output-dir ${outputDir}" when { params { - outdir = "$outputDir" + outdir = "${outputDir}" tools = 'rsem,rsem_make_transcript_fasta' } } @@ -55,7 +55,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index d9e974ff..f9a224b3 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -37,11 +37,11 @@ nextflow_pipeline { test("-profile test --tools salmon,rsem_make_transcript_fasta") { - options "-output-dir $outputDir" + options "-output-dir ${outputDir}" when { params { - outdir = "$outputDir" + outdir = "${outputDir}" tools = 'salmon,rsem_make_transcript_fasta' } } @@ -55,7 +55,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/samtools.nf.test b/tests/samtools.nf.test index 38e97634..252c5826 100644 --- a/tests/samtools.nf.test +++ b/tests/samtools.nf.test @@ -6,11 +6,11 @@ nextflow_pipeline { test("-profile test --tools faidx,intervals,sizes") { - options "-output-dir $outputDir" + options "-output-dir ${outputDir}" when { params { - outdir = "$outputDir" + outdir = "${outputDir}" tools = 'faidx,intervals,sizes' } } @@ -24,7 +24,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -55,7 +55,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -86,7 +86,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/sarek.nf.test b/tests/sarek.nf.test index d4d21075..d024cc35 100644 --- a/tests/sarek.nf.test +++ b/tests/sarek.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -56,7 +56,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/tabix.nf.test b/tests/tabix.nf.test index e08e29f7..30985434 100644 --- a/tests/tabix.nf.test +++ b/tests/tabix.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -56,7 +56,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/wbcel235.nf.test b/tests/wbcel235.nf.test index 37464f65..5b12453f 100644 --- a/tests/wbcel235.nf.test +++ b/tests/wbcel235.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_name, // All files with stable contents From 75223de23e13ee0675d6741c0bd5cb91d47b10fa Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Thu, 30 Apr 2026 11:13:51 +0200 Subject: [PATCH 11/25] code polish --- main.nf | 10 ------- tests/createsequencedictionary.nf.test | 12 ++++----- tests/default.nf.test | 4 +-- tests/hisat2.nf.test | 24 ++++++++--------- tests/kallisto.nf.test | 24 ++++++++--------- tests/multiple.nf.test | 12 ++++----- tests/rsem.nf.test | 24 ++++++++--------- tests/salmon.nf.test | 24 ++++++++--------- tests/samtools.nf.test | 36 +++++++++++++------------- tests/sarek.nf.test | 24 ++++++++--------- tests/tabix.nf.test | 24 ++++++++--------- tests/wbcel235.nf.test | 12 ++++----- 12 files changed, 110 insertions(+), 120 deletions(-) diff --git a/main.nf b/main.nf index 5dadf493..53c9b8de 100644 --- a/main.nf +++ b/main.nf @@ -163,22 +163,12 @@ workflow { ) // MODULE: MultiQC - // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report - def collated_reports = channel.empty() - .mix( - channel.topic("multiqc_files").map { _meta, _process, _tool, reports -> reports }, - NFCORE_REFERENCES.out.reports, - ) - - // MODULE: MultiQC - // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report def multiqc_report = channel.empty() // MULTIQC def multiqc_files = channel.empty() multiqc_files = multiqc_files.mix(collated_versions) - multiqc_files = multiqc_files.mix(collated_reports) def summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") def workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) diff --git a/tests/createsequencedictionary.nf.test b/tests/createsequencedictionary.nf.test index 20e30d20..b27ccce8 100644 --- a/tests/createsequencedictionary.nf.test +++ b/tests/createsequencedictionary.nf.test @@ -16,19 +16,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/default.nf.test b/tests/default.nf.test index a44220c9..e95bad42 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -21,8 +21,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions - removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", "Workflow"), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path stable_path, // All files with stable contents diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 5d7cc0dd..f01fb568 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -20,19 +20,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -53,19 +53,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 3afe67e7..c6e3a7ce 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -17,19 +17,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -47,19 +47,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/multiple.nf.test b/tests/multiple.nf.test index 039080c7..99cb8e62 100644 --- a/tests/multiple.nf.test +++ b/tests/multiple.nf.test @@ -17,19 +17,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/rsem.nf.test b/tests/rsem.nf.test index 1c12a804..03436ab0 100644 --- a/tests/rsem.nf.test +++ b/tests/rsem.nf.test @@ -17,19 +17,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -47,19 +47,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index f9a224b3..0e7ffac2 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -17,19 +17,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -47,19 +47,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/samtools.nf.test b/tests/samtools.nf.test index 252c5826..f2aa96f6 100644 --- a/tests/samtools.nf.test +++ b/tests/samtools.nf.test @@ -16,19 +16,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -47,19 +47,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -78,19 +78,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/sarek.nf.test b/tests/sarek.nf.test index d024cc35..8c8e362d 100644 --- a/tests/sarek.nf.test +++ b/tests/sarek.nf.test @@ -17,19 +17,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -48,19 +48,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/tabix.nf.test b/tests/tabix.nf.test index 30985434..595e213f 100644 --- a/tests/tabix.nf.test +++ b/tests/tabix.nf.test @@ -17,19 +17,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } @@ -48,19 +48,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/wbcel235.nf.test b/tests/wbcel235.nf.test index 5b12453f..3feba4a1 100644 --- a/tests/wbcel235.nf.test +++ b/tests/wbcel235.nf.test @@ -17,19 +17,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } From c08e14a3f991f6e259d2199f59fe96c24577c13a Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Thu, 30 Apr 2026 11:29:53 +0200 Subject: [PATCH 12/25] fix multiple vcfs --- nextflow.config | 3 ++- subworkflows/local/datasheet_to_channel/main.nf | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index b629a161..e8a16aa1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -281,7 +281,8 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-core-utils@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines + id 'nf-schema@2.7.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/subworkflows/local/datasheet_to_channel/main.nf b/subworkflows/local/datasheet_to_channel/main.nf index 89b12735..955014a1 100644 --- a/subworkflows/local/datasheet_to_channel/main.nf +++ b/subworkflows/local/datasheet_to_channel/main.nf @@ -178,7 +178,7 @@ workflow DATASHEET_TO_CHANNEL { def meta_extra = [run_tabix: meta.vcf_dbsnp_vcf_tbi || meta.vcf_dbsnp_vcf.endsWith('.vcf') ? false : true] meta_extra += [run_bgziptabix: meta.vcf_dbsnp_vcf.endsWith('.vcf') ?: false] meta_extra += [type: 'dbsnp', source_vcf: meta.vcf_dbsnp_vcf_source] - return [reduceMeta(meta) + meta_extra, meta.vcf_dbsnp_vcf.contains('{') ? file(meta.vcf_dbsnp_vcf) : meta.vcf_dbsnp_vcf] + return [reduceMeta(meta) + meta_extra, meta.vcf_dbsnp_vcf.contains('{') ? files(meta.vcf_dbsnp_vcf) : meta.vcf_dbsnp_vcf] other: true // If the reference doesn't exist, then we return nothing return null From dfb988ec630426b7868f50823109bcdefd1a92eb Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Thu, 30 Apr 2026 12:38:34 +0200 Subject: [PATCH 13/25] code polish --- main.nf | 8 +++++-- .../local/datasheet_to_channel/main.nf | 20 ++++++++-------- workflows/references.nf | 23 ++++++++----------- 3 files changed, 26 insertions(+), 25 deletions(-) diff --git a/main.nf b/main.nf index 53c9b8de..a07f41b7 100644 --- a/main.nf +++ b/main.nf @@ -274,7 +274,9 @@ workflow { path = "Annotation/${meta.source_vcf}/${file.fileName}" } - [meta + [path: "${meta.species}/${meta.source}/${meta.genome}/${path}"] - meta.subMap(invalid_keys), file] + println(path) + + [meta + [path: path] - meta.subMap(invalid_keys), file] } } @@ -283,7 +285,9 @@ output { path "multiqc" } references { - path { meta, path -> path >> meta.path } + path { meta, path -> + path >> "${meta.species}/${meta.source}/${meta.genome}/${meta.path}" + } index { path "index.json" diff --git a/subworkflows/local/datasheet_to_channel/main.nf b/subworkflows/local/datasheet_to_channel/main.nf index 955014a1..0aa1b21b 100644 --- a/subworkflows/local/datasheet_to_channel/main.nf +++ b/subworkflows/local/datasheet_to_channel/main.nf @@ -82,7 +82,7 @@ workflow DATASHEET_TO_CHANNEL { meta_extra += [run_rsem_make_transcript_fasta: meta.transcript_fasta ? false : true] meta_extra += [run_salmon: meta.salmon_index ? false : true] meta_extra += [run_star: meta.star_index ? false : true] - return [reduceMeta(meta) + meta_extra, meta.fasta] + return [reduceMeta(meta) + meta_extra, file(meta.fasta, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -103,7 +103,7 @@ workflow DATASHEET_TO_CHANNEL { file: meta.fasta_fai // If we have intervals_bed, then we don't need to run faidx def meta_extra = [run_intervals: meta.intervals_bed ? false : true] - return [reduceMeta(meta) + meta_extra, meta.fasta_fai] + return [reduceMeta(meta) + meta_extra, file(meta.fasta_fai, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -125,7 +125,7 @@ workflow DATASHEET_TO_CHANNEL { // (gff, gtf or transcript_fasta) def meta_extra = [run_gffread: meta.fasta && !meta.gtf ?: false] meta_extra += [run_hisat2: meta.splice_sites ? false : true] - return [reduceMeta(meta) + meta_extra, meta.gff] + return [reduceMeta(meta) + meta_extra, file(meta.gff, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -137,7 +137,7 @@ workflow DATASHEET_TO_CHANNEL { // If any of the reference exists, then adding run_tools to false and skip the reference creation from the annotation derived file // (gff, gtf or transcript_fasta) def meta_extra = [run_hisat2: meta.splice_sites ? false : true] - return [reduceMeta(meta) + meta_extra, meta.gtf] + return [reduceMeta(meta) + meta_extra, file(meta.gtf, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -162,7 +162,7 @@ workflow DATASHEET_TO_CHANNEL { meta_extra += [run_rsem: meta.rsem_index ? false : true] meta_extra += [run_salmon: meta.salmon_index ? false : true] meta_extra += [run_star: meta.star_index ? false : true] - return [reduceMeta(meta) + meta_extra, meta.transcript_fasta] + return [reduceMeta(meta) + meta_extra, file(meta.transcript_fasta, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -178,7 +178,7 @@ workflow DATASHEET_TO_CHANNEL { def meta_extra = [run_tabix: meta.vcf_dbsnp_vcf_tbi || meta.vcf_dbsnp_vcf.endsWith('.vcf') ? false : true] meta_extra += [run_bgziptabix: meta.vcf_dbsnp_vcf.endsWith('.vcf') ?: false] meta_extra += [type: 'dbsnp', source_vcf: meta.vcf_dbsnp_vcf_source] - return [reduceMeta(meta) + meta_extra, meta.vcf_dbsnp_vcf.contains('{') ? files(meta.vcf_dbsnp_vcf) : meta.vcf_dbsnp_vcf] + return [reduceMeta(meta) + meta_extra, files(meta.vcf_dbsnp_vcf, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -190,7 +190,7 @@ workflow DATASHEET_TO_CHANNEL { def meta_extra = [run_tabix: meta.vcf_germline_resource_vcf_tbi || meta.vcf_germline_resource_vcf.endsWith('.vcf') ? false : true] meta_extra += [run_bgziptabix: meta.vcf_germline_resource_vcf.endsWith('.vcf') ?: false] meta_extra += [type: 'germline_resource', source_vcf: meta.vcf_germline_resource_vcf_source] - return [reduceMeta(meta) + meta_extra, meta.vcf_germline_resource_vcf] + return [reduceMeta(meta) + meta_extra, file(meta.vcf_germline_resource_vcf, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -202,7 +202,7 @@ workflow DATASHEET_TO_CHANNEL { def meta_extra = [run_tabix: meta.vcf_known_indels_vcf_tbi || meta.vcf_known_indels_vcf.endsWith('.vcf') ? false : true] meta_extra += [run_bgziptabix: meta.vcf_known_indels_vcf.endsWith('.vcf') ?: false] meta_extra += [type: 'known_indels', source_vcf: meta.vcf_known_indels_vcf_source] - return [reduceMeta(meta) + meta_extra, meta.vcf_known_indels_vcf] + return [reduceMeta(meta) + meta_extra, file(meta.vcf_known_indels_vcf, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -214,7 +214,7 @@ workflow DATASHEET_TO_CHANNEL { def meta_extra = [run_tabix: meta.vcf_known_snps_vcf_tbi || meta.vcf_known_snps_vcf.endsWith('.vcf') ? false : true] meta_extra += [run_bgziptabix: meta.vcf_known_snps_vcf.endsWith('.vcf') ?: false] meta_extra += [type: 'known_snps', source_vcf: meta.vcf_known_snps_vcf_source] - return [reduceMeta(meta) + meta_extra, meta.vcf_known_snps_vcf] + return [reduceMeta(meta) + meta_extra, file(meta.vcf_known_snps_vcf, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -226,7 +226,7 @@ workflow DATASHEET_TO_CHANNEL { def meta_extra = [run_tabix: meta.vcf_pon_vcf_tbi || meta.vcf_pon_vcf.endsWith('.vcf') ? false : true] meta_extra += [run_bgziptabix: meta.vcf_pon_vcf.endsWith('.vcf') ?: false] meta_extra += [type: 'pon', source_vcf: meta.vcf_pon_vcf_source] - return [reduceMeta(meta) + meta_extra, meta.vcf_pon_vcf] + return [reduceMeta(meta) + meta_extra, file(meta.vcf_pon_vcf, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null diff --git a/workflows/references.nf b/workflows/references.nf index 6f704c8f..8336b9bd 100644 --- a/workflows/references.nf +++ b/workflows/references.nf @@ -60,31 +60,30 @@ workflow REFERENCES { tools.split(',').contains('snapaligner'), ) - // This works with a mixture of input and computed references - fasta_dict = fasta_dict.mix(PREPARE_GENOME_DNASEQ.out.fasta_dict) - fasta_fai = fasta_fai.mix(PREPARE_GENOME_DNASEQ.out.fasta_fai, PREPARE_GENOME_RNASEQ.out.fasta_fai) - fasta_sizes = fasta_sizes.mix(PREPARE_GENOME_RNASEQ.out.fasta_sizes) - gtf = gtf.mix(PREPARE_GENOME_RNASEQ.out.gtf) - intervals_bed = intervals_bed.mix(PREPARE_GENOME_DNASEQ.out.intervals_bed) - splice_sites = splice_sites.mix(PREPARE_GENOME_RNASEQ.out.splice_sites) - transcript_fasta = transcript_fasta.mix(PREPARE_GENOME_RNASEQ.out.transcript_fasta) - - // TODO: This does not work YET with a mixture of input and computed references bowtie1_index = PREPARE_GENOME_RNASEQ.out.bowtie1_index bowtie2_index = PREPARE_GENOME_RNASEQ.out.bowtie2_index bwamem1_index = PREPARE_GENOME_DNASEQ.out.bwamem1_index bwamem2_index = PREPARE_GENOME_DNASEQ.out.bwamem2_index dragmap_hashmap = PREPARE_GENOME_DNASEQ.out.dragmap_hashmap + fasta_dict = PREPARE_GENOME_DNASEQ.out.fasta_dict + fasta_fai = channel.empty().mix(PREPARE_GENOME_DNASEQ.out.fasta_fai, PREPARE_GENOME_RNASEQ.out.fasta_fai) + fasta_sizes = PREPARE_GENOME_RNASEQ.out.fasta_sizes + gtf = PREPARE_GENOME_RNASEQ.out.gtf hisat2_index = PREPARE_GENOME_RNASEQ.out.hisat2_index + intervals_bed = PREPARE_GENOME_DNASEQ.out.intervals_bed kallisto_index = PREPARE_GENOME_RNASEQ.out.kallisto_index msisensorpro_list = PREPARE_GENOME_DNASEQ.out.msisensorpro_list rsem_index = PREPARE_GENOME_RNASEQ.out.rsem_index salmon_index = PREPARE_GENOME_RNASEQ.out.salmon_index + splice_sites = PREPARE_GENOME_RNASEQ.out.splice_sites star_index = PREPARE_GENOME_RNASEQ.out.star_index + transcript_fasta = PREPARE_GENOME_RNASEQ.out.transcript_fasta vcf_tbi = PREPARE_GENOME_DNASEQ.out.vcf_tbi - // TODO: need to rescue the vcf files + // TODO: need to rescue these files + // fasta.map { meta, reference_ -> [meta + [file: 'fasta'], reference_] }, // vcf.map { meta, reference_ -> [meta + [file: "${meta.type}_vcf"], reference_] }, + // gff.map { meta, reference_ -> [meta + [file: 'gff'], reference_] }, references = channel.empty() .mix( @@ -98,11 +97,9 @@ workflow REFERENCES { bwamem2_index.map { meta, reference_ -> [meta + [file: 'bwamem2_index'], reference_] }, chr_dir.map { meta, reference_ -> [meta + [file: 'chr_dir'], reference_] }, dragmap_hashmap.map { meta, reference_ -> [meta + [file: 'dragmap_hashmap'], reference_] }, - fasta.map { meta, reference_ -> [meta + [file: 'fasta'], reference_] }, fasta_dict.map { meta, reference_ -> [meta + [file: 'fasta_dict'], reference_] }, fasta_fai.map { meta, reference_ -> [meta + [file: 'fasta_fai'], reference_] }, fasta_sizes.map { meta, reference_ -> [meta + [file: 'fasta_sizes'], reference_] }, - gff.map { meta, reference_ -> [meta + [file: 'gff'], reference_] }, gtf.map { meta, reference_ -> [meta + [file: 'gtf'], reference_] }, hisat2_index.map { meta, reference_ -> [meta + [file: 'hisat2_index'], reference_] }, intervals_bed.map { meta, reference_ -> [meta + [file: 'intervals_bed'], reference_] }, From 10c4b48134dfb5b90cb873c5065dea9b05c9762b Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Thu, 30 Apr 2026 15:13:22 +0200 Subject: [PATCH 14/25] fix ncbi --- conf/prepare_genome.config | 3 + main.nf | 56 ++++++++++----- .../ncbidatasetscli/datasets/environment.yml | 7 ++ .../local/ncbidatasetscli/datasets/main.nf | 43 ++++++++++++ .../local/ncbidatasetscli/datasets/meta.yml | 68 +++++++++++++++++++ .../local/datasheet_to_channel/main.nf | 18 ++--- .../nf-side/prepare_genome_rnaseq/main.nf | 54 +++++++-------- tests/wbcel235.nf.test.snap | 26 +++---- 8 files changed, 210 insertions(+), 65 deletions(-) create mode 100644 modules/local/ncbidatasetscli/datasets/environment.yml create mode 100644 modules/local/ncbidatasetscli/datasets/main.nf create mode 100644 modules/local/ncbidatasetscli/datasets/meta.yml diff --git a/conf/prepare_genome.config b/conf/prepare_genome.config index df05f8ed..27a8dee3 100644 --- a/conf/prepare_genome.config +++ b/conf/prepare_genome.config @@ -54,6 +54,9 @@ process { withName: 'MSISENSORPRO_SCAN' { ext.when = { meta.run_msisensorpro } } + withName: 'NCBIDATASETSCLI_DATASETS' { + ext.args = 'gff' + } withName: 'RSEM_PREPAREREFERENCE_GENOME' { ext.args = '--star' ext.when = { meta.run_rsem } diff --git a/main.nf b/main.nf index a07f41b7..14306744 100644 --- a/main.nf +++ b/main.nf @@ -15,17 +15,20 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { ARCHIVE_EXTRACT } from './subworkflows/nf-core/archive_extract' -include { DATASHEET_TO_CHANNEL } from './subworkflows/local/datasheet_to_channel' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_references_pipeline' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_references_pipeline' -include { REFERENCES } from "./workflows/references" +include { ARCHIVE_EXTRACT } from './subworkflows/nf-core/archive_extract' +include { NCBIDATASETSCLI_DATASETS as NCBIDOWNLOAD_FASTA } from './modules/local/ncbidatasetscli/datasets' +include { NCBIDATASETSCLI_DATASETS as NCBIDOWNLOAD_GFF } from './modules/local/ncbidatasetscli/datasets' +include { NCBIDATASETSCLI_DATASETS as NCBIDOWNLOAD_GTF } from './modules/local/ncbidatasetscli/datasets' +include { DATASHEET_TO_CHANNEL } from './subworkflows/local/datasheet_to_channel' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_references_pipeline' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_references_pipeline' +include { REFERENCES } from "./workflows/references" // MULTIQC & versions -include { MULTIQC } from './modules/nf-core/multiqc' -include { softwareVersionsToYAML } from 'plugin/nf-core-utils' -include { methodsDescriptionText } from './subworkflows/local/utils_nfcore_references_pipeline' -include { paramsSummaryMap } from 'plugin/nf-schema' +include { MULTIQC } from './modules/nf-core/multiqc' +include { softwareVersionsToYAML } from 'plugin/nf-core-utils' +include { methodsDescriptionText } from './subworkflows/local/utils_nfcore_references_pipeline' +include { paramsSummaryMap } from 'plugin/nf-schema' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -50,9 +53,18 @@ workflow NFCORE_REFERENCES { ascat_loci_gc_input = need_extract(DATASHEET_TO_CHANNEL.out.ascat_loci_gc, 'ascat_loci_gc') ascat_loci_rt_input = need_extract(DATASHEET_TO_CHANNEL.out.ascat_loci_rt, 'ascat_loci_rt') chr_dir_input = need_extract(DATASHEET_TO_CHANNEL.out.chr_dir, 'chr_dir') - fasta_input = need_extract(DATASHEET_TO_CHANNEL.out.fasta, 'fasta') - gff_input = need_extract(DATASHEET_TO_CHANNEL.out.gff, 'gff') - gtf_input = need_extract(DATASHEET_TO_CHANNEL.out.gtf, 'gtf') + + fasta_download_input = need_ncbi_download(DATASHEET_TO_CHANNEL.out.fasta, 'fasta') + gff_download_input = need_ncbi_download(DATASHEET_TO_CHANNEL.out.gff, 'gff') + gtf_download_input = need_ncbi_download(DATASHEET_TO_CHANNEL.out.gtf, 'gtf') + + NCBIDOWNLOAD_FASTA(fasta_download_input.to_download.map { meta, _file -> [meta + [accession: meta.source_version], 'genome'] }) + NCBIDOWNLOAD_GFF(gff_download_input.to_download.map { meta, _file -> [meta + [accession: meta.source_version], 'gff3'] }) + NCBIDOWNLOAD_GTF(gtf_download_input.to_download.map { meta, _file -> [meta + [accession: meta.source_version], 'gtf'] }) + + fasta_input = need_extract(fasta_download_input.not_downloaded, 'fasta') + gff_input = need_extract(gff_download_input.not_downloaded, 'gff') + gtf_input = need_extract(gtf_download_input.not_downloaded, 'gtf') // gather all archived references archive_to_extract = channel.empty() @@ -101,12 +113,12 @@ workflow NFCORE_REFERENCES { ascat_loci_gc_input.not_extracted.mix(extracted_reference.ascat_loci_gc), ascat_loci_rt_input.not_extracted.mix(extracted_reference.ascat_loci_rt), chr_dir_input.not_extracted.mix(extracted_reference.chr_dir), - fasta_input.not_extracted.mix(extracted_reference.fasta), + fasta_input.not_extracted.mix(extracted_reference.fasta, NCBIDOWNLOAD_FASTA.out.fna), DATASHEET_TO_CHANNEL.out.fasta_dict, DATASHEET_TO_CHANNEL.out.fasta_fai, DATASHEET_TO_CHANNEL.out.fasta_sizes, - gff_input.not_extracted.mix(extracted_reference.gff), - gtf_input.not_extracted.mix(extracted_reference.gtf), + gff_input.not_extracted.mix(extracted_reference.gff, NCBIDOWNLOAD_GFF.out.gff), + gtf_input.not_extracted.mix(extracted_reference.gtf, NCBIDOWNLOAD_GTF.out.gtf), DATASHEET_TO_CHANNEL.out.intervals_bed, DATASHEET_TO_CHANNEL.out.splice_sites, DATASHEET_TO_CHANNEL.out.transcript_fasta, @@ -274,8 +286,6 @@ workflow { path = "Annotation/${meta.source_vcf}/${file.fileName}" } - println(path) - [meta + [path: path] - meta.subMap(invalid_keys), file] } } @@ -347,3 +357,15 @@ def need_extract(channel, type) { not_extracted: true } } + +// Helper function to check if a reference needs to be downloaded from ncbi +// Add the reference type to the meta +// Depending on the extension, return the appropriate channel +def need_ncbi_download(channel, type) { + return channel + .map { meta, reference_ -> [meta + [reference: type], reference_] } + .branch { _meta, reference_ -> + to_download: reference_.toString().contains('ncbi.nlm.nih.gov') + not_downloaded: true + } +} diff --git a/modules/local/ncbidatasetscli/datasets/environment.yml b/modules/local/ncbidatasetscli/datasets/environment.yml new file mode 100644 index 00000000..18474328 --- /dev/null +++ b/modules/local/ncbidatasetscli/datasets/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge +dependencies: + - conda-forge::ncbi-datasets-cli=18.25.0 + - conda-forge::p7zip=16.02 diff --git a/modules/local/ncbidatasetscli/datasets/main.nf b/modules/local/ncbidatasetscli/datasets/main.nf new file mode 100644 index 00000000..2b30ad29 --- /dev/null +++ b/modules/local/ncbidatasetscli/datasets/main.nf @@ -0,0 +1,43 @@ +process NCBIDATASETSCLI_DATASETS { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1a/1aa4bda9c572b2003c96a5710c07d6d793f96fdea0336fa5c750be2da2e8aed6/data' + : 'community.wave.seqera.io/library/ncbi-datasets-cli_p7zip:f0c05932b8712591'}" + + input: + tuple val(meta), val(reference) + + output: + tuple val(meta), path("*enomic.gbff"), emit: gbk, optional: true + tuple val(meta), path("*enomic.fna"), emit: fna, optional: true + tuple val(meta), path("*_rm.out"), emit: rm, optional: true + tuple val(meta), path("*_feature_table.txt"), emit: features, optional: true + tuple val(meta), path("*enomic.gff"), emit: gff, optional: true + tuple val(meta), path("*enomic.gtf"), emit: gtf, optional: true + tuple val(meta), path("*rotein.faa"), emit: faa, optional: true + tuple val(meta), path("*rotein.gpff"), emit: gpff, optional: true + tuple val(meta), path("*_wgsmaster.gbff"), emit: wgs_gbk, optional: true + tuple val(meta), path("*_cds_from_genomic.fna"), emit: cds, optional: true + tuple val(meta), path("*_rna.fna"), emit: rna, optional: true + tuple val(meta), path("*_rna_from_genomic.fna"), emit: rna_fna, optional: true + tuple val(meta), path("*_assembly_report.txt"), emit: report, optional: true + tuple val(meta), path("*_assembly_stats.txt"), emit: stats, optional: true + tuple val("${task.process}"), val('ncbidatasetscli'), eval('datasets --version'), topic: versions, emit: versions_ncbidatasetscli + + when: + task.ext.when == null || task.ext.when + + script: + """ + datasets download genome accession ${meta.accession} --reference --include ${reference} + 7za \\ + x \\ + -o"data"/ \\ + ncbi_dataset.zip + + mv data/ncbi_dataset/data/${meta.accession}/* . + """ +} diff --git a/modules/local/ncbidatasetscli/datasets/meta.yml b/modules/local/ncbidatasetscli/datasets/meta.yml new file mode 100644 index 00000000..bba6b3ba --- /dev/null +++ b/modules/local/ncbidatasetscli/datasets/meta.yml @@ -0,0 +1,68 @@ +name: gunzip +description: Compresses and decompresses files. +keywords: + - gunzip + - compression + - decompression +tools: + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" + ontologies: [] +output: + gunzip: + - - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + ontologies: [] + - ${gunzip}: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + ontologies: [] + versions_gunzip: + - - ${task.process}: + type: string + description: The process the versions were collected from + - gunzip: + type: string + description: The tool name + - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - gunzip: + type: string + description: The tool name + - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + +authors: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/subworkflows/local/datasheet_to_channel/main.nf b/subworkflows/local/datasheet_to_channel/main.nf index 0aa1b21b..d5239f04 100644 --- a/subworkflows/local/datasheet_to_channel/main.nf +++ b/subworkflows/local/datasheet_to_channel/main.nf @@ -12,7 +12,7 @@ workflow DATASHEET_TO_CHANNEL { ascat_alleles_branch = datasheet.branch { meta, _readme -> file: meta.ascat_alleles - return [reduceMeta(meta), meta.ascat_alleles] + return [reduceMeta(meta), file(meta.ascat_alleles, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -21,7 +21,7 @@ workflow DATASHEET_TO_CHANNEL { ascat_loci_branch = datasheet.branch { meta, _readme -> file: meta.ascat_loci - return [reduceMeta(meta), meta.ascat_loci] + return [reduceMeta(meta), file(meta.ascat_loci, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -30,7 +30,7 @@ workflow DATASHEET_TO_CHANNEL { ascat_loci_gc_branch = datasheet.branch { meta, _readme -> file: meta.ascat_loci_gc - return [reduceMeta(meta), meta.ascat_loci_gc] + return [reduceMeta(meta), file(meta.ascat_loci_gc, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -39,7 +39,7 @@ workflow DATASHEET_TO_CHANNEL { ascat_loci_rt_branch = datasheet.branch { meta, _readme -> file: meta.ascat_loci_rt - return [reduceMeta(meta), meta.ascat_loci_rt] + return [reduceMeta(meta), file(meta.ascat_loci_rt, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -48,7 +48,7 @@ workflow DATASHEET_TO_CHANNEL { chr_dir_branch = datasheet.branch { meta, _readme -> file: meta.chr_dir - return [reduceMeta(meta), meta.chr_dir] + return [reduceMeta(meta), file(meta.chr_dir, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -57,7 +57,7 @@ workflow DATASHEET_TO_CHANNEL { intervals_bed_branch = datasheet.branch { meta, _readme -> file: meta.intervals_bed - return [reduceMeta(meta), meta.intervals_bed] + return [reduceMeta(meta), file(meta.intervals_bed, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -82,7 +82,7 @@ workflow DATASHEET_TO_CHANNEL { meta_extra += [run_rsem_make_transcript_fasta: meta.transcript_fasta ? false : true] meta_extra += [run_salmon: meta.salmon_index ? false : true] meta_extra += [run_star: meta.star_index ? false : true] - return [reduceMeta(meta) + meta_extra, file(meta.fasta, checkIfExists: true)] + return [reduceMeta(meta) + meta_extra, meta.fasta.contains('ncbi.nlm.nih.gov') ? meta.fasta : file(meta.fasta, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -125,7 +125,7 @@ workflow DATASHEET_TO_CHANNEL { // (gff, gtf or transcript_fasta) def meta_extra = [run_gffread: meta.fasta && !meta.gtf ?: false] meta_extra += [run_hisat2: meta.splice_sites ? false : true] - return [reduceMeta(meta) + meta_extra, file(meta.gff, checkIfExists: true)] + return [reduceMeta(meta) + meta_extra, meta.gtf.contains('ncbi.nlm.nih.gov') ? meta.gff : file(meta.gff, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null @@ -137,7 +137,7 @@ workflow DATASHEET_TO_CHANNEL { // If any of the reference exists, then adding run_tools to false and skip the reference creation from the annotation derived file // (gff, gtf or transcript_fasta) def meta_extra = [run_hisat2: meta.splice_sites ? false : true] - return [reduceMeta(meta) + meta_extra, file(meta.gtf, checkIfExists: true)] + return [reduceMeta(meta) + meta_extra, meta.gtf.contains('ncbi.nlm.nih.gov') ? meta.gtf : file(meta.gtf, checkIfExists: true)] other: true // If the reference doesn't exist, then we return nothing return null diff --git a/subworkflows/nf-side/prepare_genome_rnaseq/main.nf b/subworkflows/nf-side/prepare_genome_rnaseq/main.nf index 5afc1059..c5fd80e3 100644 --- a/subworkflows/nf-side/prepare_genome_rnaseq/main.nf +++ b/subworkflows/nf-side/prepare_genome_rnaseq/main.nf @@ -12,23 +12,23 @@ include { STAR_GENOMEGENERATE } from '../../.. workflow PREPARE_GENOME_RNASEQ { take: - fasta // channel: [meta, fasta] - fasta_fai // channel: [meta, fasta_fai] - gff // channel: [meta, gff] - gtf // channel: [meta, gtf] - splice_sites // channel: [meta, splice_sites] - transcript_fasta // channel: [meta, transcript_fasta] - run_bowtie1 // boolean: true/false - run_bowtie2 // boolean: true/false - run_faidx // boolean: true/false - run_hisat2 // boolean: true/false - run_hisat2_extractsplicesites // boolean: true/false - run_kallisto // boolean: true/false - run_rsem // boolean: true/false + fasta // channel: [meta, fasta] + fasta_fai // channel: [meta, fasta_fai] + gff // channel: [meta, gff] + gtf // channel: [meta, gtf] + splice_sites // channel: [meta, splice_sites] + transcript_fasta // channel: [meta, transcript_fasta] + run_bowtie1 // boolean: true/false + run_bowtie2 // boolean: true/false + run_faidx // boolean: true/false + run_hisat2 // boolean: true/false + run_hisat2_extractsplicesites // boolean: true/false + run_kallisto // boolean: true/false + run_rsem // boolean: true/false run_rsem_make_transcript_fasta // boolean: true/false - run_salmon // boolean: true/false - run_sizes // boolean: true/false - run_star // boolean: true/false + run_salmon // boolean: true/false + run_sizes // boolean: true/false + run_star // boolean: true/false main: bowtie1_index = Channel.empty() @@ -109,17 +109,17 @@ workflow PREPARE_GENOME_RNASEQ { } emit: - bowtie1_index // channel: [meta, BowtieIndex/] - bowtie2_index // channel: [meta, Bowtie2Index/] - fasta_fai // channel: [meta, *.fa(sta).fai] - fasta_sizes // channel: [meta, *.fa(sta).sizes] - gtf // channel: [meta, gtf] - hisat2_index // channel: [meta, Hisat2Index/] - kallisto_index // channel: [meta, KallistoIndex] - rsem_index // channel: [meta, RSEMIndex/] - salmon_index // channel: [meta, SalmonIndex/] - splice_sites // channel: [meta, *.splice_sites.txt] - star_index // channel: [meta, STARIndex/] + bowtie1_index // channel: [meta, BowtieIndex/] + bowtie2_index // channel: [meta, Bowtie2Index/] + fasta_fai // channel: [meta, *.fa(sta).fai] + fasta_sizes // channel: [meta, *.fa(sta).sizes] + gtf // channel: [meta, gtf] + hisat2_index // channel: [meta, Hisat2Index/] + kallisto_index // channel: [meta, KallistoIndex] + rsem_index // channel: [meta, RSEMIndex/] + salmon_index // channel: [meta, SalmonIndex/] + splice_sites // channel: [meta, *.splice_sites.txt] + star_index // channel: [meta, STARIndex/] transcript_fasta // channel: [meta, *.transcripts.fasta] topic_versions = channel.topic('versions') } diff --git a/tests/wbcel235.nf.test.snap b/tests/wbcel235.nf.test.snap index fae729ef..a54aaa34 100644 --- a/tests/wbcel235.nf.test.snap +++ b/tests/wbcel235.nf.test.snap @@ -11,8 +11,14 @@ "GATK4_CREATESEQUENCEDICTIONARY": { "gatk": "4.6.1.0" }, - "GUNZIP": { - "gunzip": 1.13 + "NCBIDOWNLOAD_FASTA": { + "ncbidatasetscli": "datasets version: 18.25.0" + }, + "NCBIDOWNLOAD_GFF": { + "ncbidatasetscli": "datasets version: 18.25.0" + }, + "NCBIDOWNLOAD_GTF": { + "ncbidatasetscli": "datasets version: 18.25.0" }, "RSEM_PREPAREREFERENCE_GENOME": { "rsem": "1.3.1", @@ -33,8 +39,7 @@ "Caenorhabditis_elegans/NCBI/WBcel235", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes", - "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/GCF_000002985.6_WBcel235_genomic.gff", - "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/GCF_000002985.6_WBcel235_genomic.gtf", + "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/genomic.gtf", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/intervals", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/intervals/WBcel235.bed", "Caenorhabditis_elegans/NCBI/WBcel235/Sequence", @@ -93,7 +98,6 @@ "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/STARIndex/GCF_000002985.6/2.7.11b/transcriptInfo.tab", "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta", "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta/GCF_000002985.6_WBcel235_genomic.dict", - "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta/GCF_000002985.6_WBcel235_genomic.fna", "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta/GCF_000002985.6_WBcel235_genomic.fna.fai", "index.json", "multiqc", @@ -110,8 +114,7 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "GCF_000002985.6_WBcel235_genomic.gff:md5,cdfa038e7ba342b73dab1e85ffdf0a4a", - "GCF_000002985.6_WBcel235_genomic.gtf:md5,efc0320858e37f3e818a392df1e07a85", + "genomic.gtf:md5,efc0320858e37f3e818a392df1e07a85", "WBcel235.bed:md5,84cb3d6e8ed7c8475fc9735b19b66908", "GCF_000002985.6_WBcel235_genomic.amb:md5,a0741fa25fb4e5a52ac61ecc5b679ac2", "GCF_000002985.6_WBcel235_genomic.ann:md5,7e46a49f983e0ca1fb6ee14be12251d3", @@ -155,15 +158,14 @@ "sjdbList.out.tab:md5,3711bf43ca770e6db6e5570c201b227b", "transcriptInfo.tab:md5,d0a2c885941c8e8920e191768a3a71dc", "GCF_000002985.6_WBcel235_genomic.dict:md5,95224495c9500f3283bbf009ffd0d990", - "GCF_000002985.6_WBcel235_genomic.fna:md5,2fa2b1575d9e722f076bafcf3b755fed", "GCF_000002985.6_WBcel235_genomic.fna.fai:md5,5765b3ad41f8ad61dc582fba226214bf", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:06:23.020458245", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T13:47:02.887729686" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } } } \ No newline at end of file From 6561e3cb264cefd54da0e92e85bf5fbfb5066d02 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Thu, 30 Apr 2026 15:40:26 +0200 Subject: [PATCH 15/25] remove unnecessary GHA --- .github/workflows/build_reference.yml | 49 -------------------- tests/hisat2.nf.test.snap | 36 +++------------ tests/kallisto.nf.test.snap | 21 +++------ tests/rsem.nf.test.snap | 66 +++------------------------ tests/salmon.nf.test.snap | 45 +++--------------- tests/samtools.nf.test.snap | 29 ++++-------- tests/sarek.nf.test.snap | 20 +++----- tests/tabix.nf.test.snap | 29 +++--------- 8 files changed, 46 insertions(+), 249 deletions(-) delete mode 100644 .github/workflows/build_reference.yml diff --git a/.github/workflows/build_reference.yml b/.github/workflows/build_reference.yml deleted file mode 100644 index 01d6c9ca..00000000 --- a/.github/workflows/build_reference.yml +++ /dev/null @@ -1,49 +0,0 @@ -name: Build reference genomes that changed -on: - push: - branches: - - main - paths: - - "assets/genomes/*.yml" - -jobs: - run-tower: - name: Run AWS full tests - if: github.repository == 'nf-core/nascent' - runs-on: ubuntu-latest - steps: - - name: Find changed genomes - id: changed-genome-files - uses: tj-actions/changed-files@v42 - with: - files: | - assets/genomes/*.yml - - name: Concatinate all the yamls together - if: steps.changed-files-specific.outputs.any_changed == 'true' - env: - CHANGED_FILES: ${{ steps.changed-files-specific.outputs.all_changed_files }} - run: cat ${CHANGED_FILES} > samplesheet.yml - # - name: Upload samplesheet.yml to s3 or Tower Datasets - # run: TODO - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_SCRATCH_BUCKET }}/work - parameters: | - { - "input": "samplesheet.yml" - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nascent/results-${{ github.sha }}" - } - profiles: cloud - - - uses: actions/upload-artifact@v4 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 4bc73609..d537b81e 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -7,22 +7,6 @@ } }, [ - "Homo_sapiens", - "Homo_sapiens/nf-core", - "Homo_sapiens/nf-core/GRCh38_chr21", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.8.ht2", - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -37,22 +21,14 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "GRCh38_chr21.1.ht2:md5,eb322cf410ecc616d7fe63cc1be2785b", - "GRCh38_chr21.2.ht2:md5,46be3356d4c236ebd5d1e52e9eaf4e12", - "GRCh38_chr21.3.ht2:md5,dbf5af96efd98d6b03f1e5d2baed848a", - "GRCh38_chr21.4.ht2:md5,bd952f748321c4c230671e8fce7b1650", - "GRCh38_chr21.5.ht2:md5,103032edf695164b32cc9e6781e8f08b", - "GRCh38_chr21.6.ht2:md5,242e36d01cd1719b6bd05f157c644eed", - "GRCh38_chr21.7.ht2:md5,24e7d0673a77e07fbe40400f9a6b3db6", - "GRCh38_chr21.8.ht2:md5,5e0626bdb7f7a267990f72ae45c3e44a", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:25:20.308458245", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:47:21.954921108" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } }, "-profile test --tools hisat2,hisat2_extractsplicesites": { "content": [ @@ -115,10 +91,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2025-10-22T13:48:24.752339407", "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:48:24.752339407" + } } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 0204bf54..fce6e852 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -46,11 +46,11 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2025-10-22T13:50:13.684163497", "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:50:13.684163497" + } }, "-profile test --tools kallisto,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ @@ -60,15 +60,6 @@ } }, [ - "Homo_sapiens", - "Homo_sapiens/nf-core", - "Homo_sapiens/nf-core/GRCh38_chr21", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM/0.51.1", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM/0.51.1/kallisto", - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -86,10 +77,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:26:45.046775001", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:48:54.722152131" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } } } \ No newline at end of file diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index fd6abe83..0f2259b4 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -8,38 +8,6 @@ } }, [ - "Homo_sapiens", - "Homo_sapiens/nf-core", - "Homo_sapiens/nf-core/GRCh38_chr21", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/Genome", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/Log.out", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/SA", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/SAindex", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrLength.txt", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrName.txt", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrNameLength.txt", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrStart.txt", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/exonInfo.tab", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/geneInfo.tab", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.chrlist", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.grp", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.idx.fa", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.seq", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.ti", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.transcripts.fa", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genomeParameters.txt", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/sjdbInfo.txt", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/sjdbList.out.tab", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/transcriptInfo.tab", - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -54,36 +22,14 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", - "Genome:md5,612664e3cfde5e1b73ad541d93752b31", - "SA:md5,074ae54177bb7b9cb981382f043f36e5", - "SAindex:md5,81a04dbb4a8366c02907ad35218d877e", - "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", - "chrName.txt:md5,e99d7d1051eee43ceab5563c2d09fcee", - "chrNameLength.txt:md5,c985a141685e8431ec27c782816cb744", - "chrStart.txt:md5,6925b594ea2eeb964ba87cd6d42ab98f", - "exonGeTrInfo.tab:md5,a36b92eeceaaf921b9d19cd8e806a98e", - "exonInfo.tab:md5,bb892190d1ebdd59bf55652916121479", - "geneInfo.tab:md5,4303e97d841035b5c0fcc3686b2f5a36", - "genome.chrlist:md5,c985a141685e8431ec27c782816cb744", - "genome.grp:md5,f75057a7bf6943f88c04f164cd641105", - "genome.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", - "genome.n2g.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", - "genome.seq:md5,03f87c5a63ec7cb6e681e8e4e042153e", - "genome.ti:md5,283306157cf36e6827e4274c896844ba", - "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", - "sjdbInfo.txt:md5,12fb05dc7cea89735a0c19e1c0df61cb", - "sjdbList.fromGTF.out.tab:md5,d9e4a184cde15a5ab282ff66e740a4a2", - "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd", - "transcriptInfo.tab:md5,ad9baa68c5432908b42693edb9aed02a", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:29:40.583485464", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:52:54.851545772" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } }, "-profile test --tools rsem,rsem_make_transcript_fasta": { "content": [ @@ -178,10 +124,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2025-10-22T13:54:31.207444454", "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:54:31.207444454" + } } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index b80a902c..0546e7ef 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -7,29 +7,6 @@ } }, [ - "Homo_sapiens", - "Homo_sapiens/nf-core", - "Homo_sapiens/nf-core/GRCh38_chr21", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/complete_ref_lens.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/ctable.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/ctg_offsets.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/info.json", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/mphf.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/pos.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/pre_indexing.log", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/rank.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/refAccumLengths.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/ref_indexing.log", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/reflengths.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/refseq.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/seq.bin", - "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/versionInfo.json", - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -44,24 +21,14 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", - "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", - "duplicate_clusters.tsv:md5,b65592e6f604234ac3cf45f8cafd8d27", - "info.json:md5,e13f6500d048a7f72bcc385ce54bd50a", - "mphf.bin:md5,9651ab954dccca304b6dcddf50fbae61", - "rank.bin:md5,e2ee4a817caa0614c7cfa732358aa829", - "refAccumLengths.bin:md5,f79c13f67c09f87982ff1503826d6350", - "reflengths.bin:md5,ec4126a76984f26dc11baa2aaec7c325", - "refseq.bin:md5,dbe45319a08f3ea4b9eed98787b683ba", - "versionInfo.json:md5,d2c799050e81aa6e282ac8a73e773941", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:31:30.540720052", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:55:46.182193326" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } }, "-profile test --tools salmon,rsem_make_transcript_fasta": { "content": [ @@ -134,10 +101,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2025-10-22T13:56:31.902100907", "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:56:31.902100907" + } } } \ No newline at end of file diff --git a/tests/samtools.nf.test.snap b/tests/samtools.nf.test.snap index 5f904c0f..c9c9a106 100644 --- a/tests/samtools.nf.test.snap +++ b/tests/samtools.nf.test.snap @@ -7,13 +7,6 @@ } }, [ - "Homo_sapiens", - "Homo_sapiens/nf-core", - "Homo_sapiens/nf-core/GRCh38_chr21", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/intervals", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/intervals/GRCh38_chr21.bed", - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -28,15 +21,14 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "GRCh38_chr21.bed:md5,472d213cfcde96565699779d5bfc0e32", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:32:44.385202648", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:57:10.974116767" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } }, "-profile test --tools faidx,intervals,sizes --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21.yml": { "content": [ @@ -44,7 +36,6 @@ }, [ - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -62,11 +53,11 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:32:57.262183628", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:57:29.976409216" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } }, "-profile test --tools faidx,intervals,sizes": { "content": [ @@ -110,10 +101,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-01-15T13:39:15.908885182", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T13:39:15.908885182" + } } } \ No newline at end of file diff --git a/tests/sarek.nf.test.snap b/tests/sarek.nf.test.snap index 95f1a0be..63bdfcbf 100644 --- a/tests/sarek.nf.test.snap +++ b/tests/sarek.nf.test.snap @@ -108,11 +108,11 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-01-15T13:40:39.747672409", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T13:40:39.747672409" + } }, "-profile test --tools bwamem1,bwamem2,createsequencedictionary,dragmap,faidx,intervals,msisensorpro,tabix --input references-datasheets/latest/genomes/Homo_sapiens/GATK/GRCh38_chr22.yml": { "content": [ @@ -122,13 +122,6 @@ } }, [ - "Homo_sapiens", - "Homo_sapiens/nf-core", - "Homo_sapiens/nf-core/GRCh38_chr22", - "Homo_sapiens/nf-core/GRCh38_chr22/Annotation", - "Homo_sapiens/nf-core/GRCh38_chr22/Annotation/msisensorpro", - "Homo_sapiens/nf-core/GRCh38_chr22/Annotation/msisensorpro/GRCh38_chr22.msisensor_scan.list", - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -143,14 +136,13 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "GRCh38_chr22.msisensor_scan.list:md5,1c670ac986f5e6d7a9d11e45231d5417", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:33:33.140511215", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:58:49.531702963" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } } } \ No newline at end of file diff --git a/tests/tabix.nf.test.snap b/tests/tabix.nf.test.snap index e0a56db4..5b149072 100644 --- a/tests/tabix.nf.test.snap +++ b/tests/tabix.nf.test.snap @@ -23,11 +23,11 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2025-10-22T13:59:06.940925897", "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:59:06.940925897" + } }, "-profile test --tools tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ @@ -40,19 +40,6 @@ } }, [ - "Homo_sapiens", - "Homo_sapiens/nf-core", - "Homo_sapiens/nf-core/GRCh38_MT", - "Homo_sapiens/nf-core/GRCh38_MT/Annotation", - "Homo_sapiens/nf-core/GRCh38_MT/Annotation/genmod_compound", - "Homo_sapiens/nf-core/GRCh38_MT/Annotation/genmod_compound/GRCh38_MT.vcf.gz.tbi", - "Homo_sapiens/nf-core/GRCh38_chr21", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE/dbsnp_146.hg38.vcf.gz.tbi", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE/gnomAD.r2.1.1.vcf.gz.tbi", - "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE/mills_and_1000G.indels.vcf.gz.tbi", - "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -67,17 +54,13 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "GRCh38_MT.vcf.gz.tbi:md5,2473d74262eddbb8ab7bceaa74f23c50", - "dbsnp_146.hg38.vcf.gz.tbi:md5,628232d0c870f2dbf73c3e81aff7b4b4", - "gnomAD.r2.1.1.vcf.gz.tbi:md5,d95bc4bd1eee441d13ed99f0f3d501f8", - "mills_and_1000G.indels.vcf.gz.tbi:md5,1bb7ab8f22eb798efd796439d3b29b7a", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-04-30T15:33:59.373289114", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T13:41:42.457020033" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } } } \ No newline at end of file From 3d0aebe07b60fb91ddd8ca55793eb24dcc31c672 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 12:55:42 +0200 Subject: [PATCH 16/25] linting --- conf/containers_conda_lock_files_amd64.config | 1 + conf/containers_conda_lock_files_arm64.config | 1 + conf/containers_docker_amd64.config | 1 + conf/containers_docker_arm64.config | 1 + .../containers_singularity_https_amd64.config | 1 + .../containers_singularity_https_arm64.config | 1 + conf/containers_singularity_oras_amd64.config | 1 + conf/containers_singularity_oras_arm64.config | 1 + modules.json | 111 +++++++++++++----- .../nf-side/prepare_genome_rnaseq/main.nf | 54 ++++----- 10 files changed, 118 insertions(+), 55 deletions(-) create mode 100644 conf/containers_conda_lock_files_amd64.config create mode 100644 conf/containers_conda_lock_files_arm64.config create mode 100644 conf/containers_docker_amd64.config create mode 100644 conf/containers_docker_arm64.config create mode 100644 conf/containers_singularity_https_amd64.config create mode 100644 conf/containers_singularity_https_arm64.config create mode 100644 conf/containers_singularity_oras_amd64.config create mode 100644 conf/containers_singularity_oras_arm64.config diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config new file mode 100644 index 00000000..f487ba40 --- /dev/null +++ b/conf/containers_conda_lock_files_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config new file mode 100644 index 00000000..e9a3fedc --- /dev/null +++ b/conf/containers_conda_lock_files_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config new file mode 100644 index 00000000..01b59df5 --- /dev/null +++ b/conf/containers_docker_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config new file mode 100644 index 00000000..7785cb13 --- /dev/null +++ b/conf/containers_docker_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config new file mode 100644 index 00000000..754821b3 --- /dev/null +++ b/conf/containers_singularity_https_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config new file mode 100644 index 00000000..93071de8 --- /dev/null +++ b/conf/containers_singularity_https_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config new file mode 100644 index 00000000..952881d8 --- /dev/null +++ b/conf/containers_singularity_oras_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config new file mode 100644 index 00000000..498ec506 --- /dev/null +++ b/conf/containers_singularity_oras_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } diff --git a/modules.json b/modules.json index 195c1371..aaa2bc27 100644 --- a/modules.json +++ b/modules.json @@ -8,22 +8,30 @@ "gunzip": { "branch": "master", "git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c", - "installed_by": ["archive_extract"] + "installed_by": [ + "archive_extract" + ] }, "multiqc": { "branch": "master", "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["archive_extract"] + "installed_by": [ + "archive_extract" + ] }, "unzip": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["archive_extract"] + "installed_by": [ + "archive_extract" + ] } } }, @@ -32,7 +40,9 @@ "archive_extract": { "branch": "master", "git_sha": "1298fbd2004c2913d6682ce4a419647d97a8fc3f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } @@ -43,97 +53,136 @@ "bowtie/build": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "bowtie2/build": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "bwa/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "bwamem2/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "dragmap/hashtable": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "gatk4/createsequencedictionary": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "gawk": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "gffread": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "hisat2/build": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "hisat2/extractsplicesites": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "kallisto/index": { "branch": "main", "git_sha": "4b418e22f9fb3a5e753fcf4224baf12d445ff7b9", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "msisensorpro/scan": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "rsem/preparereference": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "salmon/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "samtools/faidx": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq", "prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_dnaseq", + "prepare_genome_rnaseq" + ] }, "snapaligner/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "star/genomegenerate": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_rnaseq"] + "installed_by": [ + "prepare_genome_rnaseq" + ] }, "tabix/bgziptabix": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] }, "tabix/tabix": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["prepare_genome_dnaseq"] + "installed_by": [ + "prepare_genome_dnaseq" + ] } } }, @@ -142,20 +191,26 @@ "prepare_genome_dnaseq": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "prepare_genome_rnaseq": { "branch": "main", "git_sha": "4b418e22f9fb3a5e753fcf4224baf12d445ff7b9", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_references": { "branch": "main", "git_sha": "3f81209f8ae9b11925da2a9a8bc57bfdb5028eef", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/subworkflows/nf-side/prepare_genome_rnaseq/main.nf b/subworkflows/nf-side/prepare_genome_rnaseq/main.nf index c5fd80e3..5afc1059 100644 --- a/subworkflows/nf-side/prepare_genome_rnaseq/main.nf +++ b/subworkflows/nf-side/prepare_genome_rnaseq/main.nf @@ -12,23 +12,23 @@ include { STAR_GENOMEGENERATE } from '../../.. workflow PREPARE_GENOME_RNASEQ { take: - fasta // channel: [meta, fasta] - fasta_fai // channel: [meta, fasta_fai] - gff // channel: [meta, gff] - gtf // channel: [meta, gtf] - splice_sites // channel: [meta, splice_sites] - transcript_fasta // channel: [meta, transcript_fasta] - run_bowtie1 // boolean: true/false - run_bowtie2 // boolean: true/false - run_faidx // boolean: true/false - run_hisat2 // boolean: true/false - run_hisat2_extractsplicesites // boolean: true/false - run_kallisto // boolean: true/false - run_rsem // boolean: true/false + fasta // channel: [meta, fasta] + fasta_fai // channel: [meta, fasta_fai] + gff // channel: [meta, gff] + gtf // channel: [meta, gtf] + splice_sites // channel: [meta, splice_sites] + transcript_fasta // channel: [meta, transcript_fasta] + run_bowtie1 // boolean: true/false + run_bowtie2 // boolean: true/false + run_faidx // boolean: true/false + run_hisat2 // boolean: true/false + run_hisat2_extractsplicesites // boolean: true/false + run_kallisto // boolean: true/false + run_rsem // boolean: true/false run_rsem_make_transcript_fasta // boolean: true/false - run_salmon // boolean: true/false - run_sizes // boolean: true/false - run_star // boolean: true/false + run_salmon // boolean: true/false + run_sizes // boolean: true/false + run_star // boolean: true/false main: bowtie1_index = Channel.empty() @@ -109,17 +109,17 @@ workflow PREPARE_GENOME_RNASEQ { } emit: - bowtie1_index // channel: [meta, BowtieIndex/] - bowtie2_index // channel: [meta, Bowtie2Index/] - fasta_fai // channel: [meta, *.fa(sta).fai] - fasta_sizes // channel: [meta, *.fa(sta).sizes] - gtf // channel: [meta, gtf] - hisat2_index // channel: [meta, Hisat2Index/] - kallisto_index // channel: [meta, KallistoIndex] - rsem_index // channel: [meta, RSEMIndex/] - salmon_index // channel: [meta, SalmonIndex/] - splice_sites // channel: [meta, *.splice_sites.txt] - star_index // channel: [meta, STARIndex/] + bowtie1_index // channel: [meta, BowtieIndex/] + bowtie2_index // channel: [meta, Bowtie2Index/] + fasta_fai // channel: [meta, *.fa(sta).fai] + fasta_sizes // channel: [meta, *.fa(sta).sizes] + gtf // channel: [meta, gtf] + hisat2_index // channel: [meta, Hisat2Index/] + kallisto_index // channel: [meta, KallistoIndex] + rsem_index // channel: [meta, RSEMIndex/] + salmon_index // channel: [meta, SalmonIndex/] + splice_sites // channel: [meta, *.splice_sites.txt] + star_index // channel: [meta, STARIndex/] transcript_fasta // channel: [meta, *.transcripts.fasta] topic_versions = channel.topic('versions') } From 0af5408e5f6f9086d0946d2d966e6aba15e534b1 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 4 May 2026 13:10:19 +0200 Subject: [PATCH 17/25] Apply suggestion from @maxulysse --- CITATIONS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index 07e602f6..57750a7e 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -54,7 +54,7 @@ - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) -> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. - [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/) From 7974525245c94b156b87f47c675f2c8f7587f32d Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 13:12:33 +0200 Subject: [PATCH 18/25] modules update --- modules.json | 111 +++++++++++++-------------------------------------- 1 file changed, 28 insertions(+), 83 deletions(-) diff --git a/modules.json b/modules.json index aaa2bc27..195c1371 100644 --- a/modules.json +++ b/modules.json @@ -8,30 +8,22 @@ "gunzip": { "branch": "master", "git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c", - "installed_by": [ - "archive_extract" - ] + "installed_by": ["archive_extract"] }, "multiqc": { "branch": "master", "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": [ - "archive_extract" - ] + "installed_by": ["archive_extract"] }, "unzip": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": [ - "archive_extract" - ] + "installed_by": ["archive_extract"] } } }, @@ -40,9 +32,7 @@ "archive_extract": { "branch": "master", "git_sha": "1298fbd2004c2913d6682ce4a419647d97a8fc3f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } @@ -53,136 +43,97 @@ "bowtie/build": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "bowtie2/build": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "bwa/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "bwamem2/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "dragmap/hashtable": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "gatk4/createsequencedictionary": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "gawk": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "gffread": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "hisat2/build": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "hisat2/extractsplicesites": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "kallisto/index": { "branch": "main", "git_sha": "4b418e22f9fb3a5e753fcf4224baf12d445ff7b9", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "msisensorpro/scan": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "rsem/preparereference": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "salmon/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "samtools/faidx": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq", - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_dnaseq", "prepare_genome_rnaseq"] }, "snapaligner/index": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "star/genomegenerate": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_rnaseq" - ] + "installed_by": ["prepare_genome_rnaseq"] }, "tabix/bgziptabix": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] }, "tabix/tabix": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "prepare_genome_dnaseq" - ] + "installed_by": ["prepare_genome_dnaseq"] } } }, @@ -191,26 +142,20 @@ "prepare_genome_dnaseq": { "branch": "main", "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "prepare_genome_rnaseq": { "branch": "main", "git_sha": "4b418e22f9fb3a5e753fcf4224baf12d445ff7b9", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_references": { "branch": "main", "git_sha": "3f81209f8ae9b11925da2a9a8bc57bfdb5028eef", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 1658b11ee6824b58b73562d5bdb50437262ad5b4 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 13:19:48 +0200 Subject: [PATCH 19/25] lint --- conf/containers_conda_lock_files_amd64.config | 1 - conf/containers_conda_lock_files_arm64.config | 1 - conf/containers_docker_amd64.config | 1 - conf/containers_docker_arm64.config | 1 - conf/containers_singularity_https_amd64.config | 1 - conf/containers_singularity_https_arm64.config | 1 - conf/containers_singularity_oras_amd64.config | 1 - conf/containers_singularity_oras_arm64.config | 1 - 8 files changed, 8 deletions(-) delete mode 100644 conf/containers_conda_lock_files_amd64.config delete mode 100644 conf/containers_conda_lock_files_arm64.config delete mode 100644 conf/containers_docker_amd64.config delete mode 100644 conf/containers_docker_arm64.config delete mode 100644 conf/containers_singularity_https_amd64.config delete mode 100644 conf/containers_singularity_https_arm64.config delete mode 100644 conf/containers_singularity_oras_amd64.config delete mode 100644 conf/containers_singularity_oras_arm64.config diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config deleted file mode 100644 index f487ba40..00000000 --- a/conf/containers_conda_lock_files_amd64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config deleted file mode 100644 index e9a3fedc..00000000 --- a/conf/containers_conda_lock_files_arm64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config deleted file mode 100644 index 01b59df5..00000000 --- a/conf/containers_docker_amd64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config deleted file mode 100644 index 7785cb13..00000000 --- a/conf/containers_docker_arm64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config deleted file mode 100644 index 754821b3..00000000 --- a/conf/containers_singularity_https_amd64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config deleted file mode 100644 index 93071de8..00000000 --- a/conf/containers_singularity_https_arm64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config deleted file mode 100644 index 952881d8..00000000 --- a/conf/containers_singularity_oras_amd64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config deleted file mode 100644 index 498ec506..00000000 --- a/conf/containers_singularity_oras_arm64.config +++ /dev/null @@ -1 +0,0 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } From 121e2870b419796e33de6596123e689f55a03549 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 4 May 2026 13:21:53 +0200 Subject: [PATCH 20/25] Apply suggestion from @maxulysse --- conf/prepare_genome.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/conf/prepare_genome.config b/conf/prepare_genome.config index 27a8dee3..df05f8ed 100644 --- a/conf/prepare_genome.config +++ b/conf/prepare_genome.config @@ -54,9 +54,6 @@ process { withName: 'MSISENSORPRO_SCAN' { ext.when = { meta.run_msisensorpro } } - withName: 'NCBIDATASETSCLI_DATASETS' { - ext.args = 'gff' - } withName: 'RSEM_PREPAREREFERENCE_GENOME' { ext.args = '--star' ext.when = { meta.run_rsem } From 4a327849a613213c8ecfd56ded983bf41ad51a56 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 13:52:28 +0200 Subject: [PATCH 21/25] update tests and snpashots --- nextflow.config | 1 + nextflow_schema.json | 7 +++++++ tests/createsequencedictionary.nf.test | 2 ++ tests/createsequencedictionary.nf.test.snap | 9 +++++---- tests/default.nf.test | 2 ++ tests/default.nf.test.snap | 9 +++++---- tests/hisat2.nf.test | 4 ++++ tests/hisat2.nf.test.snap | 10 ++++++---- tests/kallisto.nf.test | 4 ++++ tests/kallisto.nf.test.snap | 10 ++++++---- tests/multiple.nf.test | 4 ++++ tests/multiple.nf.test.snap | 18 ++++++++++-------- tests/rsem.nf.test | 4 ++++ tests/rsem.nf.test.snap | 10 ++++++---- tests/salmon.nf.test | 4 ++++ tests/salmon.nf.test.snap | 10 ++++++---- tests/samtools.nf.test | 6 ++++++ tests/samtools.nf.test.snap | 13 ++++++++----- tests/sarek.nf.test | 4 ++++ tests/sarek.nf.test.snap | 10 ++++++---- tests/tabix.nf.test | 4 ++++ tests/tabix.nf.test.snap | 10 ++++++---- tests/wbcel235.nf.test | 2 ++ tests/wbcel235.nf.test.snap | 3 ++- 24 files changed, 114 insertions(+), 46 deletions(-) diff --git a/nextflow.config b/nextflow.config index e8a16aa1..8c466359 100644 --- a/nextflow.config +++ b/nextflow.config @@ -34,6 +34,7 @@ params { show_hidden = false version = false references_base_path = null + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') diff --git a/nextflow_schema.json b/nextflow_schema.json index 61a4fe22..83a606b4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -193,6 +193,13 @@ "fa_icon": "fas fa-check-square", "hidden": true }, + "modules_testdata_base_path": { + "type": "string", + "fa_icon": "far fa-check-circle", + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/", + "hidden": true + }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", diff --git a/tests/createsequencedictionary.nf.test b/tests/createsequencedictionary.nf.test index b27ccce8..c109da99 100644 --- a/tests/createsequencedictionary.nf.test +++ b/tests/createsequencedictionary.nf.test @@ -23,6 +23,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/createsequencedictionary.nf.test.snap b/tests/createsequencedictionary.nf.test.snap index 7338aca4..d58c75ee 100644 --- a/tests/createsequencedictionary.nf.test.snap +++ b/tests/createsequencedictionary.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools createsequencedictionary": { "content": [ + 2, { "GATK4_CREATESEQUENCEDICTIONARY": { "gatk": "4.6.1.0" @@ -32,10 +33,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-05-04T13:25:57.485529971", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" - }, - "timestamp": "2025-10-22T13:44:32.157311293" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } } } \ No newline at end of file diff --git a/tests/default.nf.test b/tests/default.nf.test index e95bad42..baf8d395 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -21,6 +21,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4669744b..5d61f771 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test": { "content": [ + 6, { "BOWTIE1_BUILD": { "bowtie": "1.3.1" @@ -112,10 +113,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-05-04T13:27:00.400984209", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T13:26:42.652887516" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index f01fb568..eb492a58 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -27,6 +27,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -60,6 +62,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index d537b81e..2a2d1b1b 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools hisat2,hisat2_extractsplicesites --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ + 2, { "HISAT2_BUILD": { "hisat2": "2.2.1" @@ -24,7 +25,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:25:20.308458245", + "timestamp": "2026-05-04T13:28:33.954930393", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" @@ -32,6 +33,7 @@ }, "-profile test --tools hisat2,hisat2_extractsplicesites": { "content": [ + 4, { "GFFREAD": { "gffread": "0.12.7" @@ -91,10 +93,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2025-10-22T13:48:24.752339407", + "timestamp": "2026-05-04T13:30:01.145090085", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } } } \ No newline at end of file diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index c6e3a7ce..9ede214c 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -54,6 +56,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index fce6e852..6c2a93ab 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools kallisto,rsem_make_transcript_fasta": { "content": [ + 4, { "GFFREAD": { "gffread": "0.12.7" @@ -46,14 +47,15 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2025-10-22T13:50:13.684163497", + "timestamp": "2026-05-04T13:32:55.770278716", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } }, "-profile test --tools kallisto,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ + 2, { "KALLISTO_INDEX": { "kallisto": "0.51.1" @@ -77,7 +79,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:26:45.046775001", + "timestamp": "2026-05-04T13:50:57.360101913", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" diff --git a/tests/multiple.nf.test b/tests/multiple.nf.test index 99cb8e62..e9a94b7f 100644 --- a/tests/multiple.nf.test +++ b/tests/multiple.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -55,6 +57,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/multiple.nf.test.snap b/tests/multiple.nf.test.snap index 37a55aa5..cddc2121 100644 --- a/tests/multiple.nf.test.snap +++ b/tests/multiple.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools bwamem1,createsequencedictionary,faidx,intervals --input references-datasheets/latest/genomes_source/Homo_sapiens/nf-core/GRCh38_chr21_chr22.yml": { "content": [ + 9, { "BUILD_INTERVALS": { "gawk": "5.3.0" @@ -82,14 +83,15 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-05-04T13:34:18.615057144", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T13:32:53.633810585" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } }, "-profile test --tools tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/GATK/GRCh37_GRCh38_multiple_dbsnps_globs.yml": { "content": [ + 5, { "TABIX_TABIX": { "tabix": "1.21" @@ -130,10 +132,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-05-04T13:34:53.027597524", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T13:33:25.90199516" + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } } } \ No newline at end of file diff --git a/tests/rsem.nf.test b/tests/rsem.nf.test index 03436ab0..295cc8ad 100644 --- a/tests/rsem.nf.test +++ b/tests/rsem.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -54,6 +56,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index 0f2259b4..6519fa31 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools rsem,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ + 2, { "RSEM_PREPAREREFERENCE_GENOME": { "rsem": "1.3.1", @@ -25,7 +26,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:29:40.583485464", + "timestamp": "2026-05-04T13:36:09.996427896", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" @@ -33,6 +34,7 @@ }, "-profile test --tools rsem,rsem_make_transcript_fasta": { "content": [ + 4, { "GFFREAD": { "gffread": "0.12.7" @@ -124,10 +126,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2025-10-22T13:54:31.207444454", + "timestamp": "2026-05-04T13:37:36.256698472", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } } } \ No newline at end of file diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 0e7ffac2..51536db1 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -54,6 +56,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 0546e7ef..4de93022 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools salmon,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ + 2, { "SALMON_INDEX": { "salmon": "1.10.3" @@ -24,7 +25,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:31:30.540720052", + "timestamp": "2026-05-04T13:39:03.494523804", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" @@ -32,6 +33,7 @@ }, "-profile test --tools salmon,rsem_make_transcript_fasta": { "content": [ + 4, { "GFFREAD": { "gffread": "0.12.7" @@ -101,10 +103,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2025-10-22T13:56:31.902100907", + "timestamp": "2026-05-04T13:40:03.501871668", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } } } \ No newline at end of file diff --git a/tests/samtools.nf.test b/tests/samtools.nf.test index f2aa96f6..fd47cbfd 100644 --- a/tests/samtools.nf.test +++ b/tests/samtools.nf.test @@ -23,6 +23,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -54,6 +56,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -85,6 +89,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/samtools.nf.test.snap b/tests/samtools.nf.test.snap index c9c9a106..bec14d4e 100644 --- a/tests/samtools.nf.test.snap +++ b/tests/samtools.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools faidx,intervals,sizes --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ + 2, { "BUILD_INTERVALS": { "gawk": "5.3.0" @@ -24,7 +25,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:32:44.385202648", + "timestamp": "2026-05-04T13:40:47.675835575", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" @@ -32,6 +33,7 @@ }, "-profile test --tools faidx,intervals,sizes --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21.yml": { "content": [ + 1, { }, @@ -53,7 +55,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:32:57.262183628", + "timestamp": "2026-05-04T13:41:05.353083125", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" @@ -61,6 +63,7 @@ }, "-profile test --tools faidx,intervals,sizes": { "content": [ + 3, { "BUILD_INTERVALS": { "gawk": "5.3.0" @@ -101,10 +104,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-01-15T13:39:15.908885182", + "timestamp": "2026-05-04T13:40:27.407837236", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } } } \ No newline at end of file diff --git a/tests/sarek.nf.test b/tests/sarek.nf.test index 8c8e362d..cfd5e059 100644 --- a/tests/sarek.nf.test +++ b/tests/sarek.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -55,6 +57,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/sarek.nf.test.snap b/tests/sarek.nf.test.snap index 63bdfcbf..0cc32416 100644 --- a/tests/sarek.nf.test.snap +++ b/tests/sarek.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools bwamem1,bwamem2,createsequencedictionary,dragmap,faidx,intervals,msisensorpro,tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/GATK/GRCh38_chr22.yml": { "content": [ + 11, { "BUILD_INTERVALS": { "gawk": "5.3.0" @@ -108,14 +109,15 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-01-15T13:40:39.747672409", + "timestamp": "2026-05-04T13:41:28.713575532", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } }, "-profile test --tools bwamem1,bwamem2,createsequencedictionary,dragmap,faidx,intervals,msisensorpro,tabix --input references-datasheets/latest/genomes/Homo_sapiens/GATK/GRCh38_chr22.yml": { "content": [ + 2, { "MSISENSORPRO_SCAN": { "msisensor-pro": "1.3.0" @@ -139,7 +141,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:33:33.140511215", + "timestamp": "2026-05-04T13:41:52.912833324", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" diff --git a/tests/tabix.nf.test b/tests/tabix.nf.test index 595e213f..d78376d4 100644 --- a/tests/tabix.nf.test +++ b/tests/tabix.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path @@ -55,6 +57,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/tabix.nf.test.snap b/tests/tabix.nf.test.snap index 5b149072..af35b434 100644 --- a/tests/tabix.nf.test.snap +++ b/tests/tabix.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/nf-core/GRCh38_chr21_chr22.yml": { "content": [ + 1, { }, @@ -23,14 +24,15 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2025-10-22T13:59:06.940925897", + "timestamp": "2026-05-04T13:49:48.65709389", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } }, "-profile test --tools tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { "content": [ + 5, { "TABIX_BGZIPTABIX": { "tabix": "1.21" @@ -57,7 +59,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:33:59.373289114", + "timestamp": "2026-05-04T13:42:21.061901802", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" diff --git a/tests/wbcel235.nf.test b/tests/wbcel235.nf.test index 3feba4a1..e0e51563 100644 --- a/tests/wbcel235.nf.test +++ b/tests/wbcel235.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { assert workflow.success assertAll( { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'), // All stable path name, with a relative path diff --git a/tests/wbcel235.nf.test.snap b/tests/wbcel235.nf.test.snap index a54aaa34..4d18db86 100644 --- a/tests/wbcel235.nf.test.snap +++ b/tests/wbcel235.nf.test.snap @@ -1,6 +1,7 @@ { "-profile test --tools bwamem1,createsequencedictionary,faidx,intervals,rsem,star --input Caenorhabditis_elegans/NCBI/WBcel235.yml": { "content": [ + 10, { "BUILD_INTERVALS": { "gawk": "5.3.0" @@ -162,7 +163,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-04-30T15:06:23.020458245", + "timestamp": "2026-05-04T13:47:32.099507695", "meta": { "nf-test": "0.9.5", "nextflow": "26.03.4" From e797d5fc753f5718d74f620b3d8843b5703195c5 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 14:11:09 +0200 Subject: [PATCH 22/25] minimal NFX_VERSION bump --- .github/workflows/nf-test.yml | 4 ++-- README.md | 2 +- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 69d60f82..13d9851d 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -78,8 +78,8 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "25.10.4" - - "latest-everything" + - 26.04.0 + - latest-everything env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} diff --git a/README.md b/README.md index d76d4f16..e4d3aaa4 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14576225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14576225) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) [![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) diff --git a/nextflow.config b/nextflow.config index 8c466359..01b7afe1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -275,7 +275,7 @@ manifest { description = """help community build references""" mainScript = 'main.nf' defaultBranch = 'main' - nextflowVersion = '!>=25.10.4' + nextflowVersion = '!>=26.04.0' version = '0.2' doi = '10.5281/zenodo.14576225' } From add0909f2c83401b59ece6a1d57ea650268049ea Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 16:17:43 +0200 Subject: [PATCH 23/25] fix publishing --- .gitignore | 3 +- main.nf | 9 +++--- tests/hisat2.nf.test.snap | 28 ++++++++++++++++-- tests/kallisto.nf.test.snap | 17 ++++++++--- tests/rsem.nf.test.snap | 58 +++++++++++++++++++++++++++++++++++-- tests/salmon.nf.test.snap | 37 +++++++++++++++++++++-- tests/samtools.nf.test.snap | 17 ++++++++--- tests/sarek.nf.test.snap | 16 +++++++--- tests/tabix.nf.test.snap | 21 ++++++++++++-- tests/wbcel235.nf.test.snap | 8 +++-- workflows/references.nf | 6 ++-- 11 files changed, 189 insertions(+), 31 deletions(-) diff --git a/.gitignore b/.gitignore index e010de7a..50d43c8c 100644 --- a/.gitignore +++ b/.gitignore @@ -13,4 +13,5 @@ null/ tmp/ .nf-test .vscode -modules/nf +modules/nf-*/**/tests/ +subworkflows/nf-*/**/tests/ \ No newline at end of file diff --git a/main.nf b/main.nf index 14306744..ab9440c1 100644 --- a/main.nf +++ b/main.nf @@ -218,7 +218,7 @@ workflow { publish: multiqc = MULTIQC.out.data.mix(MULTIQC.out.plots, MULTIQC.out.report) - references = NFCORE_REFERENCES.out.references.filter { _meta, file -> !(file instanceof String) }.map { meta, file -> + references = NFCORE_REFERENCES.out.references.filter { _meta, file -> !(file instanceof String) }.filter { _meta, file -> !(file.toString().startsWith('/nf-core')) }.map { meta, file -> // Filter out the run_ keys from the meta for a clearer index file def invalid_keys = meta.keySet().findAll { key -> key.startsWith('run_') } @@ -295,14 +295,13 @@ output { path "multiqc" } references { - path { meta, path -> - path >> "${meta.species}/${meta.source}/${meta.genome}/${meta.path}" - } - index { path "index.json" sep ":" } + path { meta, path -> + path >> "${meta.species}/${meta.source}/${meta.genome}/${meta.path}" + } } } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 2a2d1b1b..0cd40402 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -8,6 +8,22 @@ } }, [ + "Homo_sapiens", + "Homo_sapiens/nf-core", + "Homo_sapiens/nf-core/GRCh38_chr21", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.1.ht2", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.2.ht2", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.3.ht2", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.4.ht2", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.5.ht2", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.6.ht2", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.7.ht2", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/2.2.1/GRCh38_chr21.8.ht2", + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -22,13 +38,21 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "GRCh38_chr21.1.ht2:md5,eb322cf410ecc616d7fe63cc1be2785b", + "GRCh38_chr21.2.ht2:md5,46be3356d4c236ebd5d1e52e9eaf4e12", + "GRCh38_chr21.3.ht2:md5,dbf5af96efd98d6b03f1e5d2baed848a", + "GRCh38_chr21.4.ht2:md5,bd952f748321c4c230671e8fce7b1650", + "GRCh38_chr21.5.ht2:md5,103032edf695164b32cc9e6781e8f08b", + "GRCh38_chr21.6.ht2:md5,242e36d01cd1719b6bd05f157c644eed", + "GRCh38_chr21.7.ht2:md5,24e7d0673a77e07fbe40400f9a6b3db6", + "GRCh38_chr21.8.ht2:md5,5e0626bdb7f7a267990f72ae45c3e44a", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:28:33.954930393", + "timestamp": "2026-05-04T16:03:12.129814483", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } }, "-profile test --tools hisat2,hisat2_extractsplicesites": { diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 6c2a93ab..86d0b5e1 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -47,10 +47,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:32:55.770278716", + "timestamp": "2026-05-04T15:57:10.384204424", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } }, "-profile test --tools kallisto,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": { @@ -62,6 +62,15 @@ } }, [ + "Homo_sapiens", + "Homo_sapiens/nf-core", + "Homo_sapiens/nf-core/GRCh38_chr21", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM/0.51.1", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM/0.51.1/kallisto", + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -79,10 +88,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:50:57.360101913", + "timestamp": "2026-05-04T15:56:50.407246621", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index 6519fa31..ede21148 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -9,6 +9,38 @@ } }, [ + "Homo_sapiens", + "Homo_sapiens/nf-core", + "Homo_sapiens/nf-core/GRCh38_chr21", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/GRCh38_chr21.fa", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/Genome", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/Log.out", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/SA", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/SAindex", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrLength.txt", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrName.txt", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrNameLength.txt", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/chrStart.txt", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/exonInfo.tab", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/geneInfo.tab", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.chrlist", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.grp", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.idx.fa", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.n2g.idx.fa", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.seq", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.ti", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genome.transcripts.fa", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/genomeParameters.txt", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/sjdbInfo.txt", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/sjdbList.out.tab", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/1.3.1/transcriptInfo.tab", + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -23,13 +55,35 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", + "Genome:md5,612664e3cfde5e1b73ad541d93752b31", + "SA:md5,074ae54177bb7b9cb981382f043f36e5", + "SAindex:md5,81a04dbb4a8366c02907ad35218d877e", + "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", + "chrName.txt:md5,e99d7d1051eee43ceab5563c2d09fcee", + "chrNameLength.txt:md5,c985a141685e8431ec27c782816cb744", + "chrStart.txt:md5,6925b594ea2eeb964ba87cd6d42ab98f", + "exonGeTrInfo.tab:md5,a36b92eeceaaf921b9d19cd8e806a98e", + "exonInfo.tab:md5,bb892190d1ebdd59bf55652916121479", + "geneInfo.tab:md5,4303e97d841035b5c0fcc3686b2f5a36", + "genome.chrlist:md5,c985a141685e8431ec27c782816cb744", + "genome.grp:md5,f75057a7bf6943f88c04f164cd641105", + "genome.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", + "genome.n2g.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", + "genome.seq:md5,03f87c5a63ec7cb6e681e8e4e042153e", + "genome.ti:md5,283306157cf36e6827e4274c896844ba", + "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", + "sjdbInfo.txt:md5,12fb05dc7cea89735a0c19e1c0df61cb", + "sjdbList.fromGTF.out.tab:md5,d9e4a184cde15a5ab282ff66e740a4a2", + "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd", + "transcriptInfo.tab:md5,ad9baa68c5432908b42693edb9aed02a", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:36:09.996427896", + "timestamp": "2026-05-04T16:06:44.791909632", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } }, "-profile test --tools rsem,rsem_make_transcript_fasta": { diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 4de93022..4780df6e 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -8,6 +8,29 @@ } }, [ + "Homo_sapiens", + "Homo_sapiens/nf-core", + "Homo_sapiens/nf-core/GRCh38_chr21", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/complete_ref_lens.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/ctable.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/ctg_offsets.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/duplicate_clusters.tsv", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/info.json", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/mphf.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/pos.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/pre_indexing.log", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/rank.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/refAccumLengths.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/ref_indexing.log", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/reflengths.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/refseq.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/seq.bin", + "Homo_sapiens/nf-core/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/1.10.3/versionInfo.json", + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -22,13 +45,23 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", + "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", + "duplicate_clusters.tsv:md5,b65592e6f604234ac3cf45f8cafd8d27", + "info.json:md5,e13f6500d048a7f72bcc385ce54bd50a", + "mphf.bin:md5,9651ab954dccca304b6dcddf50fbae61", + "rank.bin:md5,e2ee4a817caa0614c7cfa732358aa829", + "refAccumLengths.bin:md5,f79c13f67c09f87982ff1503826d6350", + "reflengths.bin:md5,ec4126a76984f26dc11baa2aaec7c325", + "refseq.bin:md5,dbe45319a08f3ea4b9eed98787b683ba", + "versionInfo.json:md5,d2c799050e81aa6e282ac8a73e773941", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:39:03.494523804", + "timestamp": "2026-05-04T16:09:11.675553276", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } }, "-profile test --tools salmon,rsem_make_transcript_fasta": { diff --git a/tests/samtools.nf.test.snap b/tests/samtools.nf.test.snap index bec14d4e..e6a4af75 100644 --- a/tests/samtools.nf.test.snap +++ b/tests/samtools.nf.test.snap @@ -8,6 +8,13 @@ } }, [ + "Homo_sapiens", + "Homo_sapiens/nf-core", + "Homo_sapiens/nf-core/GRCh38_chr21", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/intervals", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/intervals/GRCh38_chr21.bed", + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -22,13 +29,14 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "GRCh38_chr21.bed:md5,472d213cfcde96565699779d5bfc0e32", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:40:47.675835575", + "timestamp": "2026-05-04T16:10:30.34680381", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } }, "-profile test --tools faidx,intervals,sizes --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21.yml": { @@ -38,6 +46,7 @@ }, [ + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -55,10 +64,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:41:05.353083125", + "timestamp": "2026-05-04T16:10:43.92484123", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } }, "-profile test --tools faidx,intervals,sizes": { diff --git a/tests/sarek.nf.test.snap b/tests/sarek.nf.test.snap index 0cc32416..abce54df 100644 --- a/tests/sarek.nf.test.snap +++ b/tests/sarek.nf.test.snap @@ -109,10 +109,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:41:28.713575532", + "timestamp": "2026-05-04T15:57:51.433637102", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } }, "-profile test --tools bwamem1,bwamem2,createsequencedictionary,dragmap,faidx,intervals,msisensorpro,tabix --input references-datasheets/latest/genomes/Homo_sapiens/GATK/GRCh38_chr22.yml": { @@ -124,6 +124,13 @@ } }, [ + "Homo_sapiens", + "Homo_sapiens/nf-core", + "Homo_sapiens/nf-core/GRCh38_chr22", + "Homo_sapiens/nf-core/GRCh38_chr22/Annotation", + "Homo_sapiens/nf-core/GRCh38_chr22/Annotation/msisensorpro", + "Homo_sapiens/nf-core/GRCh38_chr22/Annotation/msisensorpro/GRCh38_chr22.msisensor_scan.list", + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -138,13 +145,14 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "GRCh38_chr22.msisensor_scan.list:md5,1c670ac986f5e6d7a9d11e45231d5417", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:41:52.912833324", + "timestamp": "2026-05-04T16:00:36.157261789", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/tests/tabix.nf.test.snap b/tests/tabix.nf.test.snap index af35b434..3f62ee6f 100644 --- a/tests/tabix.nf.test.snap +++ b/tests/tabix.nf.test.snap @@ -42,6 +42,19 @@ } }, [ + "Homo_sapiens", + "Homo_sapiens/nf-core", + "Homo_sapiens/nf-core/GRCh38_MT", + "Homo_sapiens/nf-core/GRCh38_MT/Annotation", + "Homo_sapiens/nf-core/GRCh38_MT/Annotation/genmod_compound", + "Homo_sapiens/nf-core/GRCh38_MT/Annotation/genmod_compound/GRCh38_MT.vcf.gz.tbi", + "Homo_sapiens/nf-core/GRCh38_chr21", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE/dbsnp_146.hg38.vcf.gz.tbi", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE/gnomAD.r2.1.1.vcf.gz.tbi", + "Homo_sapiens/nf-core/GRCh38_chr21/Annotation/GATK_BUNDLE/mills_and_1000G.indels.vcf.gz.tbi", + "index.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/llms-full.txt", @@ -56,13 +69,17 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "GRCh38_MT.vcf.gz.tbi:md5,2473d74262eddbb8ab7bceaa74f23c50", + "dbsnp_146.hg38.vcf.gz.tbi:md5,628232d0c870f2dbf73c3e81aff7b4b4", + "gnomAD.r2.1.1.vcf.gz.tbi:md5,d95bc4bd1eee441d13ed99f0f3d501f8", + "mills_and_1000G.indels.vcf.gz.tbi:md5,1bb7ab8f22eb798efd796439d3b29b7a", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:42:21.061901802", + "timestamp": "2026-05-04T16:11:10.049971239", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/tests/wbcel235.nf.test.snap b/tests/wbcel235.nf.test.snap index 4d18db86..0243ad55 100644 --- a/tests/wbcel235.nf.test.snap +++ b/tests/wbcel235.nf.test.snap @@ -40,6 +40,7 @@ "Caenorhabditis_elegans/NCBI/WBcel235", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes", + "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/genomic.gff", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/genomic.gtf", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/intervals", "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/intervals/WBcel235.bed", @@ -99,6 +100,7 @@ "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/STARIndex/GCF_000002985.6/2.7.11b/transcriptInfo.tab", "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta", "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta/GCF_000002985.6_WBcel235_genomic.dict", + "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta/GCF_000002985.6_WBcel235_genomic.fna", "Caenorhabditis_elegans/NCBI/WBcel235/Sequence/WholeGenomeFasta/GCF_000002985.6_WBcel235_genomic.fna.fai", "index.json", "multiqc", @@ -115,6 +117,7 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "genomic.gff:md5,cdfa038e7ba342b73dab1e85ffdf0a4a", "genomic.gtf:md5,efc0320858e37f3e818a392df1e07a85", "WBcel235.bed:md5,84cb3d6e8ed7c8475fc9735b19b66908", "GCF_000002985.6_WBcel235_genomic.amb:md5,a0741fa25fb4e5a52ac61ecc5b679ac2", @@ -159,14 +162,15 @@ "sjdbList.out.tab:md5,3711bf43ca770e6db6e5570c201b227b", "transcriptInfo.tab:md5,d0a2c885941c8e8920e191768a3a71dc", "GCF_000002985.6_WBcel235_genomic.dict:md5,95224495c9500f3283bbf009ffd0d990", + "GCF_000002985.6_WBcel235_genomic.fna:md5,2fa2b1575d9e722f076bafcf3b755fed", "GCF_000002985.6_WBcel235_genomic.fna.fai:md5,5765b3ad41f8ad61dc582fba226214bf", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T13:47:32.099507695", + "timestamp": "2026-05-04T16:16:02.502102917", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/workflows/references.nf b/workflows/references.nf index 8336b9bd..bd8a5e8d 100644 --- a/workflows/references.nf +++ b/workflows/references.nf @@ -66,7 +66,7 @@ workflow REFERENCES { bwamem2_index = PREPARE_GENOME_DNASEQ.out.bwamem2_index dragmap_hashmap = PREPARE_GENOME_DNASEQ.out.dragmap_hashmap fasta_dict = PREPARE_GENOME_DNASEQ.out.fasta_dict - fasta_fai = channel.empty().mix(PREPARE_GENOME_DNASEQ.out.fasta_fai, PREPARE_GENOME_RNASEQ.out.fasta_fai) + fasta_fai = PREPARE_GENOME_DNASEQ.out.fasta_fai fasta_sizes = PREPARE_GENOME_RNASEQ.out.fasta_sizes gtf = PREPARE_GENOME_RNASEQ.out.gtf hisat2_index = PREPARE_GENOME_RNASEQ.out.hisat2_index @@ -81,9 +81,7 @@ workflow REFERENCES { vcf_tbi = PREPARE_GENOME_DNASEQ.out.vcf_tbi // TODO: need to rescue these files - // fasta.map { meta, reference_ -> [meta + [file: 'fasta'], reference_] }, // vcf.map { meta, reference_ -> [meta + [file: "${meta.type}_vcf"], reference_] }, - // gff.map { meta, reference_ -> [meta + [file: 'gff'], reference_] }, references = channel.empty() .mix( @@ -97,9 +95,11 @@ workflow REFERENCES { bwamem2_index.map { meta, reference_ -> [meta + [file: 'bwamem2_index'], reference_] }, chr_dir.map { meta, reference_ -> [meta + [file: 'chr_dir'], reference_] }, dragmap_hashmap.map { meta, reference_ -> [meta + [file: 'dragmap_hashmap'], reference_] }, + fasta.map { meta, reference_ -> [meta + [file: 'fasta'], reference_] }, fasta_dict.map { meta, reference_ -> [meta + [file: 'fasta_dict'], reference_] }, fasta_fai.map { meta, reference_ -> [meta + [file: 'fasta_fai'], reference_] }, fasta_sizes.map { meta, reference_ -> [meta + [file: 'fasta_sizes'], reference_] }, + gff.map { meta, reference_ -> [meta + [file: 'gff'], reference_] }, gtf.map { meta, reference_ -> [meta + [file: 'gtf'], reference_] }, hisat2_index.map { meta, reference_ -> [meta + [file: 'hisat2_index'], reference_] }, intervals_bed.map { meta, reference_ -> [meta + [file: 'intervals_bed'], reference_] }, From affc87df1d2e0a4886048d3a6f78b8b7825f4071 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 16:30:15 +0200 Subject: [PATCH 24/25] better local modules --- modules/local/ncbidatasetscli/datasets/main.nf | 12 +----------- modules/local/ncbidatasetscli/datasets/meta.yml | 14 ++++++-------- modules/nf-core/gunzip/main.nf | 8 ++++---- tests/wbcel235.nf.test.snap | 5 ++++- 4 files changed, 15 insertions(+), 24 deletions(-) diff --git a/modules/local/ncbidatasetscli/datasets/main.nf b/modules/local/ncbidatasetscli/datasets/main.nf index 2b30ad29..9fdbf7fd 100644 --- a/modules/local/ncbidatasetscli/datasets/main.nf +++ b/modules/local/ncbidatasetscli/datasets/main.nf @@ -11,21 +11,11 @@ process NCBIDATASETSCLI_DATASETS { tuple val(meta), val(reference) output: - tuple val(meta), path("*enomic.gbff"), emit: gbk, optional: true tuple val(meta), path("*enomic.fna"), emit: fna, optional: true - tuple val(meta), path("*_rm.out"), emit: rm, optional: true - tuple val(meta), path("*_feature_table.txt"), emit: features, optional: true tuple val(meta), path("*enomic.gff"), emit: gff, optional: true tuple val(meta), path("*enomic.gtf"), emit: gtf, optional: true - tuple val(meta), path("*rotein.faa"), emit: faa, optional: true - tuple val(meta), path("*rotein.gpff"), emit: gpff, optional: true - tuple val(meta), path("*_wgsmaster.gbff"), emit: wgs_gbk, optional: true - tuple val(meta), path("*_cds_from_genomic.fna"), emit: cds, optional: true - tuple val(meta), path("*_rna.fna"), emit: rna, optional: true - tuple val(meta), path("*_rna_from_genomic.fna"), emit: rna_fna, optional: true - tuple val(meta), path("*_assembly_report.txt"), emit: report, optional: true - tuple val(meta), path("*_assembly_stats.txt"), emit: stats, optional: true tuple val("${task.process}"), val('ncbidatasetscli'), eval('datasets --version'), topic: versions, emit: versions_ncbidatasetscli + tuple val("${task.process}"), val('gunzip'), eval('gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//"'), topic: versions, emit: versions_gunzip when: task.ext.when == null || task.ext.when diff --git a/modules/local/ncbidatasetscli/datasets/meta.yml b/modules/local/ncbidatasetscli/datasets/meta.yml index bba6b3ba..500d6adc 100644 --- a/modules/local/ncbidatasetscli/datasets/meta.yml +++ b/modules/local/ncbidatasetscli/datasets/meta.yml @@ -1,11 +1,9 @@ -name: gunzip +name: ncbi-datasets-cli description: Compresses and decompresses files. keywords: - - gunzip - - compression - - decompression + - ncbi-datasets-cli tools: - - gunzip: + - ncbi-datasets-cli: description: | gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html @@ -17,9 +15,9 @@ input: description: | Optional groovy Map containing meta information e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed + - reference: + type: string + description: reference to download pattern: "*.*" ontologies: [] output: diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 6edffc59..11912a9a 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -20,8 +20,8 @@ process GUNZIP { script: def args = task.ext.args ?: '' def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name - def extension = file(nameWithoutGz).extension - def name = file(nameWithoutGz).baseName + def extension = file(nameWithoutGz).extension + def name = file(nameWithoutGz).baseName def prefix = task.ext.prefix ?: name gunzip = prefix + ".${extension}" """ @@ -37,8 +37,8 @@ process GUNZIP { stub: def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name - def extension = file(nameWithoutGz).extension - def name = file(nameWithoutGz).baseName + def extension = file(nameWithoutGz).extension + def name = file(nameWithoutGz).baseName def prefix = task.ext.prefix ?: name gunzip = prefix + ".${extension}" """ diff --git a/tests/wbcel235.nf.test.snap b/tests/wbcel235.nf.test.snap index 0243ad55..f84da148 100644 --- a/tests/wbcel235.nf.test.snap +++ b/tests/wbcel235.nf.test.snap @@ -13,12 +13,15 @@ "gatk": "4.6.1.0" }, "NCBIDOWNLOAD_FASTA": { + "gunzip": "1.12", "ncbidatasetscli": "datasets version: 18.25.0" }, "NCBIDOWNLOAD_GFF": { + "gunzip": "1.12", "ncbidatasetscli": "datasets version: 18.25.0" }, "NCBIDOWNLOAD_GTF": { + "gunzip": "1.12", "ncbidatasetscli": "datasets version: 18.25.0" }, "RSEM_PREPAREREFERENCE_GENOME": { @@ -167,7 +170,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-05-04T16:16:02.502102917", + "timestamp": "2026-05-04T16:26:31.767288789", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 871c0d584d0963b896ba64240be76c4557446968 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 4 May 2026 16:40:28 +0200 Subject: [PATCH 25/25] code polish --- .gitignore | 2 +- modules/nf-core/gunzip/main.nf | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 50d43c8c..a35a3b66 100644 --- a/.gitignore +++ b/.gitignore @@ -14,4 +14,4 @@ tmp/ .nf-test .vscode modules/nf-*/**/tests/ -subworkflows/nf-*/**/tests/ \ No newline at end of file +subworkflows/nf-*/**/tests/ diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 11912a9a..6edffc59 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -20,8 +20,8 @@ process GUNZIP { script: def args = task.ext.args ?: '' def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name - def extension = file(nameWithoutGz).extension - def name = file(nameWithoutGz).baseName + def extension = file(nameWithoutGz).extension + def name = file(nameWithoutGz).baseName def prefix = task.ext.prefix ?: name gunzip = prefix + ".${extension}" """ @@ -37,8 +37,8 @@ process GUNZIP { stub: def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name - def extension = file(nameWithoutGz).extension - def name = file(nameWithoutGz).baseName + def extension = file(nameWithoutGz).extension + def name = file(nameWithoutGz).baseName def prefix = task.ext.prefix ?: name gunzip = prefix + ".${extension}" """