From 7b0d7845486575ac0473b4c00a6efefedd1c2d40 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Wed, 28 Feb 2024 14:47:29 +0100 Subject: [PATCH 01/17] =?UTF-8?q?bump=20pipeline=20version=20to=201.2.0dev?= =?UTF-8?q?=20-=20LAT=C3=9CRNICH?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- CHANGELOG.md | 2 ++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fac25536..c2b4f13c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ 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). +## 1.2.0dev - LATÜRNICH + ## 1.1.0 - Schmuddlweddr This release mostly contains updates of the respective modules. Functional updates are the following: diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 8bd71204..e3d29f8d 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/pangenome + This report has been generated by the nf-core/pangenome analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-pangenome-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 5acdc2e7..96de2087 100644 --- a/nextflow.config +++ b/nextflow.config @@ -276,7 +276,7 @@ manifest { description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.0' + version = '1.2.0dev' doi = 'https://doi.org/10.5281/zenodo.8202636' } From cf1a29b2c66dd9e55beee71d9eb7cbb8ad0c32d2 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 29 Feb 2024 16:11:15 +0000 Subject: [PATCH 02/17] Template update for nf-core/tools version 2.13.1 --- .devcontainer/devcontainer.json | 10 +---- .github/CONTRIBUTING.md | 14 ++++--- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/ci.yml | 2 +- .github/workflows/download_pipeline.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .gitpod.yml | 6 +-- CHANGELOG.md | 2 +- README.md | 3 +- 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 | 12 +++--- nextflow.config | 2 +- .../utils_nfcore_pangenome_pipeline/main.nf | 10 +++-- .../tests/main.function.nf.test | 2 +- .../tests/main.function.nf.test.snap | 12 +++++- .../tests/main.workflow.nf.test | 20 ++------- .../tests/nextflow.config | 2 +- .../tests/main.function.nf.test.snap | 42 +++++++++++++++---- .../tests/main.workflow.nf.test.snap | 6 ++- .../tests/main.nf.test | 2 +- 25 files changed, 101 insertions(+), 76 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..b290e090 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,15 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.defaultInterpreterPath": "/opt/conda/bin/python" }, // Add the IDs of extensions you want installed when the container is created. diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 5f77d235..b7eab72e 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,9 +9,8 @@ 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 ;) -:::info -If you need help using or modifying nf-core/pangenome then the best place to ask is on the nf-core Slack [#pangenome](https://nfcore.slack.com/channels/pangenome) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: +> [!NOTE] +> If you need help using or modifying nf-core/pangenome then the best place to ask is on the nf-core Slack [#pangenome](https://nfcore.slack.com/channels/pangenome) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow @@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +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. @@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`. 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. -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. +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 diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 5658d1a1..e6620d62 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pang - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pangenome/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/pangenome _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7f891f43..9695be11 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@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 @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index bd5d1bc8..8ee95d63 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8fec3877..7f4c1de2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index f823210d..08622fd5 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 748b4311..073e1876 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c3674af2..d468aeaa 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: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.gitpod.yml b/.gitpod.yml index 363d5b1d..105a1821 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -10,13 +10,11 @@ tasks: vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - 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 + # - 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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 77849c44..ffabf168 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). -## v1.1.0dev - [date] +## v1.2.0dev - [date] Initial release of nf-core/pangenome, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 3fa46acc..08833ad3 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,13 @@ [![GitHub Actions CI Status](https://github.com/nf-core/pangenome/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pangenome/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/pangenome/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pangenome/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/pangenome/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/) [![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 Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/pangenome) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/pangenome) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pangenome-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pangenome)[![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) diff --git a/modules.json b/modules.json index 2914d0d4..5dde8be3 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2212096a..ca39fb67 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 354f4430..47ac352f 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:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--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 c204b488..bfebd802 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,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:28:51.744211298" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:28.847433492" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:13.223621555" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 96493a24..f809be68 100644 --- a/nextflow.config +++ b/nextflow.config @@ -231,7 +231,7 @@ manifest { description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.0dev' + version = '1.2.0dev' doi = '' } diff --git a/subworkflows/local/utils_nfcore_pangenome_pipeline/main.nf b/subworkflows/local/utils_nfcore_pangenome_pipeline/main.nf index dc90ad90..28231f8c 100644 --- a/subworkflows/local/utils_nfcore_pangenome_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pangenome_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// Subworkflow with functionality specific to the nf-core/pangenome pipeline // /* @@ -152,7 +152,9 @@ workflow PIPELINE_COMPLETION { // def validateInputParameters() { genomeExistsError() -}// +} + +// // Validate channels from input samplesheet // def validateInputSamplesheet(input) { @@ -190,7 +192,9 @@ def genomeExistsError() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } -}// +} + +// // Generate methods description for MultiQC // def toolCitationText() { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310c..68718e4f 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f8..e3f0baf4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file 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 f7c54bc6..ca964ce8 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 @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -68,19 +62,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +87,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ffe..d0a926bf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -6,4 +6,4 @@ manifest { nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} 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 10f948e6..1037232c 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 @@ -1,25 +1,41 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "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" ], - "timestamp": "2024-01-19T11:34:38.840454873" + "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" ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" }, "Test Function without logColours": { "content": [ @@ -73,13 +89,21 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function dashedLine": { "content": [ "-\u001b[2m----------------------------------------------------\u001b[0m-" ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" }, "Test Function with logColours": { "content": [ @@ -133,6 +157,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54c..859d1030 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "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_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 517ee54e..5784a33f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -197,4 +197,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +} From a68f506854a79b88f96de92077b8e0a552b9a775 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Wed, 6 Mar 2024 11:22:50 +0100 Subject: [PATCH 03/17] fix wfmash v0.12.6 parameters --- conf/modules.config | 12 ++++++++---- nextflow.config | 1 + nextflow_schema.json | 5 +++++ workflows/pangenome.nf | 2 +- 4 files changed, 15 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index a69540b5..c5dc2c4e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -102,7 +102,7 @@ process { withName: WFMASH_MAP_ALIGN { ext.args = { [ - "-n ${params.n_haplotypes - 1}", + "-n ${params.wfmash_n_mappings}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -114,6 +114,7 @@ process { "${wfmash_sparse_map_cmd}", params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", "-2 ${params.wfmash_hg_filter_ani_diff}", + "--lower-triangular", ].join(" ").trim() } publishDir = [ @@ -126,7 +127,7 @@ process { withName: WFMASH_MAP { ext.args = { [ - "-n ${params.n_haplotypes - 1}", + "-n ${params.wfmash_n_mappings}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -139,6 +140,7 @@ process { params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", "-m", "-2 ${params.wfmash_hg_filter_ani_diff}", + "--lower-triangular", ].join(" ").trim() } publishDir = [ @@ -151,7 +153,7 @@ process { withName: WFMASH_MAP_COMMUNITY { ext.args = { [ - "-n ${params.n_haplotypes - 1}", + "-n ${params.wfmash_n_mappings}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -164,6 +166,7 @@ process { params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", "-m", "-2 ${params.wfmash_hg_filter_ani_diff}", + "--lower-triangular", ].join(" ").trim() } publishDir = [ @@ -185,7 +188,7 @@ process { withName: WFMASH_ALIGN { ext.args = { [ - "-n ${params.n_haplotypes - 1}", + "-n ${params.wfmash_n_mappings}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -198,6 +201,7 @@ process { params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", "--invert-filtering", "-2 ${params.wfmash_hg_filter_ani_diff}", + "--lower-triangular", ].join(" ").trim() } publishDir = [ diff --git a/nextflow.config b/nextflow.config index 96de2087..d0d726c7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,6 +27,7 @@ params { wfmash_only = false wfmash_temp_dir = null wfmash_hg_filter_ani_diff = 30 + wfmash_n_mappings = 1 // Seqwish options seqwish_paf = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 2b6a4a07..884f43fa 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -119,6 +119,11 @@ "type": "integer", "default": 30, "description": "Filter out mappings unlikely to be this Average Nucleotide Identity (ANI) less than the best mapping." + }, + "wfmash_n_mappings": { + "type": "integer", + "default": 1, + "description": "Number of mappings for each segment." } } }, diff --git a/workflows/pangenome.nf b/workflows/pangenome.nf index c75684fa..dc4d7c84 100644 --- a/workflows/pangenome.nf +++ b/workflows/pangenome.nf @@ -132,7 +132,7 @@ workflow PANGENOME { ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) if (!params.communities) { if (!params.wfmash_only) { - ch_multiqc_files = ch_multiqc_files.mix(PGGB.out.qc.map{return it[1..8]}) + ch_multiqc_files = ch_multiqc_files.mix(PGGB.out.qc.map{return it[1..9]}) } } else { ch_multiqc_files = ch_multiqc_files.mix(ODGI_QC.out.qc.map{return it[1..8]}) From 355329f5f375ee1dd88363405b750d92dfa6827b Mon Sep 17 00:00:00 2001 From: subwaystation Date: Wed, 6 Mar 2024 15:21:23 +0100 Subject: [PATCH 04/17] give smoothxg more threads in hla.config --- conf/hla.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/hla.config b/conf/hla.config index 9e3c6572..d7c8f8ab 100644 --- a/conf/hla.config +++ b/conf/hla.config @@ -15,7 +15,7 @@ process { } withName:'SMOOTHXG' { - cpus = 4 + cpus = 8 memory = 8.GB // container = "ghcr.io/pangenome/pggb:20230331171956507fc0" } From b9ffbeb0915dc3e77f1252ce065c3d5368982dfa Mon Sep 17 00:00:00 2001 From: subwaystation Date: Wed, 6 Mar 2024 15:22:02 +0100 Subject: [PATCH 05/17] revert vg version back to 1.40 and update vg deconstruct code --- .github/workflows/ci.yml | 4 ++-- modules/local/vg_deconstruct/main.nf | 14 +++++++++----- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 68cba8e8..77c0ee19 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,7 +50,7 @@ jobs: strategy: matrix: parameters: - - '--vcf_spec "gi|568815561:#,gi|568815567:#"' + - '--vcf_spec "gi|568815561:5,gi|568815567:25"' steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -164,7 +164,7 @@ jobs: parameters: - "--communities" - "--communities --wfmash_chunks 2" - - '--communities --vcf_spec "gi|568815561:#,gi|568815567:#"' + - '--communities --vcf_spec "gi|568815561:5,gi|568815567:25"' steps: - name: Check out pipeline code uses: actions/checkout@v3 diff --git a/modules/local/vg_deconstruct/main.nf b/modules/local/vg_deconstruct/main.nf index ae6092f0..c3557ba4 100644 --- a/modules/local/vg_deconstruct/main.nf +++ b/modules/local/vg_deconstruct/main.nf @@ -29,7 +29,7 @@ process VG_DECONSTRUCT { 'https://depot.galaxyproject.org/singularity/pggb:0.5.3--hdfd78af_2': 'quay.io/biocontainers/pggb:0.5.3--hdfd78af_2' }" */ - container "ghcr.io/pangenome/pggb:20230819064109936a2c" + container "ghcr.io/pangenome/pggb:202402032147026ffe7f" input: tuple val(meta), path(graph), val(vcf_spec) @@ -47,16 +47,20 @@ process VG_DECONSTRUCT { def prefix = task.ext.prefix ?: "${meta.id}" """ ref=\$(echo "$vcf_spec" | cut -f 1 -d:) - delim=\$(echo "$vcf_spec" | cut -f 2 -d:) - pop_length=\$(echo "$vcf_spec" | cut -f 3 -d:) + if [[ "$vcf_spec" == *":"* ]]; then + pop_length=\$(echo "$vcf_spec" | cut -f 2 -d:) + else + pop_length="" + fi if [[ -z \$pop_length ]]; then pop_length=0 fi vcf="${graph}".\$(echo \$ref | tr '/|' '_').vcf - vg deconstruct -P \$ref -H \$delim -e -a -t "${task.cpus}" "${graph}" > \$vcf + vg deconstruct -P \$ref -H "#" -e -a -t "${task.cpus}" "${graph}" > \$vcf bcftools stats \$vcf > \$vcf.stats + if [[ \$pop_length -gt 0 ]]; then vcf_decomposed=${graph}.final.\$(echo \$ref | tr '/|' '_').decomposed.vcf vcf_decomposed_tmp=\$vcf_decomposed.tmp.vcf @@ -65,7 +69,7 @@ process VG_DECONSTRUCT { #TODO: to remove when vcfwave will be bug-free # The TYPE info sometimes is wrong/missing # There are variants without the ALT allele - bcftools sort \$vcf_decomposed_tmp | bcftools annotate -x INFO/TYPE \$vcf_decomposed_tmp | awk '\$5 != "."' > \$vcf_decomposed + bcftools sort \$vcf_decomposed_tmp | bcftools annotate -x INFO/TYPE | awk '\$5 != "."' > \$vcf_decomposed rm \$vcf_decomposed_tmp \$vcf.gz bcftools stats \$vcf_decomposed > \$vcf_decomposed.stats fi From fae571a920bcb05c880305aea6038e0a0ac70b5a Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Wed, 6 Mar 2024 15:39:14 +0100 Subject: [PATCH 06/17] Update nextflow.config Bug --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 27862a9d..a2e73f1d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -296,7 +296,7 @@ def check_max(obj, type) { return obj } } else if (type == 'time') { - try {4 + try { if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) return params.max_time as nextflow.util.Duration else From 9250435a6bc9979e044c1886dec814b6ec2e213c Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Wed, 6 Mar 2024 15:41:38 +0100 Subject: [PATCH 07/17] Update nextflow.config --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index a2e73f1d..96de2087 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,6 +278,7 @@ manifest { nextflowVersion = '!>=23.04.0' version = '1.2.0dev' doi = 'https://doi.org/10.5281/zenodo.8202636' +} // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' From d8f2aa7b04d004d7da52d9e5a9cb161ef5fa8da7 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Wed, 13 Mar 2024 13:32:12 +0100 Subject: [PATCH 08/17] bump bcftools to 1.19 --- modules/local/vg_deconstruct/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/vg_deconstruct/main.nf b/modules/local/vg_deconstruct/main.nf index c3557ba4..237747cd 100644 --- a/modules/local/vg_deconstruct/main.nf +++ b/modules/local/vg_deconstruct/main.nf @@ -29,7 +29,7 @@ process VG_DECONSTRUCT { 'https://depot.galaxyproject.org/singularity/pggb:0.5.3--hdfd78af_2': 'quay.io/biocontainers/pggb:0.5.3--hdfd78af_2' }" */ - container "ghcr.io/pangenome/pggb:202402032147026ffe7f" + container "ghcr.io/pangenome/pggb:20240313103308d2dc38" input: tuple val(meta), path(graph), val(vcf_spec) From 19ecf0040391d83d6df2fe4b329710a65193a70f Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 14 Mar 2024 11:13:15 +0100 Subject: [PATCH 09/17] prepare 1.1.1 release --- CHANGELOG.md | 8 +++++++- README.md | 2 ++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 4 files changed, 12 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c2b4f13c..83b83040 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,13 @@ 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). -## 1.2.0dev - LATÜRNICH +## 1.1.1 - LATÜRNICH + +This release fixes some important bugs: + +- Per default, we set the number of mappings in `wfmash` to `1`. Previously, this was set to the given number of haplotypes. +- To complement the issue above, there is a new parameter `wfmash_n_mappings` with default `1`. +- `bcftools` in the `VG_DECONSTRUCT` module was updated to the most recent version `1.19` to prevent errors like `corrupted size vs. prev_size`. ## 1.1.0 - Schmuddlweddr diff --git a/README.md b/README.md index 722779e2..796efedf 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,8 @@ [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pangenome-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pangenome)[![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) +> WARNING: Version 1.1.0 does contain some known bugs. It is recommended to directly use version 1.1.1. For details please take a look at [CHANGELOG.md](CHANGELOG.md). + ## Introduction **nf-core/pangenome** is a bioinformatics best-practice analysis pipeline for pangenome graph construction. The pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e3d29f8d..c6b56005 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/pangenome + This report has been generated by the nf-core/pangenome analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-pangenome-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index d0d726c7..ec06325d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -277,7 +277,7 @@ manifest { description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.2.0dev' + version = '1.1.1' doi = 'https://doi.org/10.5281/zenodo.8202636' } From fe7d639492de0cff143f4312a903ce2c600782de Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 14 Mar 2024 11:29:25 +0100 Subject: [PATCH 10/17] reflect vcf_spec changes also in the schema --- CHANGELOG.md | 1 + nextflow_schema.json | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 83b83040..8b5db7d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ This release fixes some important bugs: - Per default, we set the number of mappings in `wfmash` to `1`. Previously, this was set to the given number of haplotypes. - To complement the issue above, there is a new parameter `wfmash_n_mappings` with default `1`. - `bcftools` in the `VG_DECONSTRUCT` module was updated to the most recent version `1.19` to prevent errors like `corrupted size vs. prev_size`. +- Fixed some problems with the delimiter in `VG_DECONSTRUCT` so that the parameters given by `--vcf-spec` are now applied correctly. ## 1.1.0 - Schmuddlweddr diff --git a/nextflow_schema.json b/nextflow_schema.json index 884f43fa..2af5dcb3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -260,8 +260,8 @@ "properties": { "vcf_spec": { "type": "string", - "description": "Specify a set of VCFs to produce with --vcf_spec \"REF:DELIM[:LEN][,REF:DELIM:[LEN]]*\".", - "help_text": "The paths matching ^REF are used as a reference, while the sample haplotypes are derived from path names, e.g. when DELIM=# and with '-V chm13:#', a path named HG002#1#ctg would be assigned to sample HG002 phase 1. If LEN is specified and greater than 0, the VCFs are decomposed, filtering sites whose max allele length is greater than LEN." + "description": "Specify a set of VCFs to produce with --vcf_spec \"REF[:LEN][,REF[:LEN]]*\".", + "help_text": "The paths matching ^REF are used as a reference, while the sample haplotypes are derived from path names, e.g. when DELIM=# and with '-V chm13', a path named HG002#1#ctg would be assigned to sample HG002 phase 1. If LEN is specified and greater than 0, the VCFs are decomposed, filtering sites whose max allele length is greater than LEN." } } }, From 0ee3458c52910b7567f140f1ff77ec27f939ea23 Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Thu, 14 Mar 2024 12:00:05 +0100 Subject: [PATCH 11/17] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8b5db7d7..27150aa2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ This release fixes some important bugs: - To complement the issue above, there is a new parameter `wfmash_n_mappings` with default `1`. - `bcftools` in the `VG_DECONSTRUCT` module was updated to the most recent version `1.19` to prevent errors like `corrupted size vs. prev_size`. - Fixed some problems with the delimiter in `VG_DECONSTRUCT` so that the parameters given by `--vcf-spec` are now applied correctly. +- Updated to nf-core template version 2.13.1 ## 1.1.0 - Schmuddlweddr From b2cb539591463bdb200e7854302651ce7f474682 Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Thu, 14 Mar 2024 12:00:35 +0100 Subject: [PATCH 12/17] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 2af5dcb3..225ef49d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -261,7 +261,7 @@ "vcf_spec": { "type": "string", "description": "Specify a set of VCFs to produce with --vcf_spec \"REF[:LEN][,REF[:LEN]]*\".", - "help_text": "The paths matching ^REF are used as a reference, while the sample haplotypes are derived from path names, e.g. when DELIM=# and with '-V chm13', a path named HG002#1#ctg would be assigned to sample HG002 phase 1. If LEN is specified and greater than 0, the VCFs are decomposed, filtering sites whose max allele length is greater than LEN." + "help_text": "The paths matching `^REF` are used as a reference, while the sample haplotypes are derived from path names, e.g. when `DELIM=#` and with `-V chm13`, a path named HG002#1#ctg would be assigned to sample HG002 phase 1. If `LEN` is specified and greater than 0, the VCFs are decomposed, filtering sites whose max allele length is greater than `LEN`." } } }, From b9434e3d2731cda7af3bf641c15d30d2c2debabe Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 14 Mar 2024 12:01:53 +0100 Subject: [PATCH 13/17] remove warning as suggested by review --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index 796efedf..722779e2 100644 --- a/README.md +++ b/README.md @@ -16,8 +16,6 @@ [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pangenome-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pangenome)[![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) -> WARNING: Version 1.1.0 does contain some known bugs. It is recommended to directly use version 1.1.1. For details please take a look at [CHANGELOG.md](CHANGELOG.md). - ## Introduction **nf-core/pangenome** is a bioinformatics best-practice analysis pipeline for pangenome graph construction. The pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs. From c19f69aeb18d5006cb8d2fe60ab732edeb8b24ea Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Thu, 14 Mar 2024 12:02:14 +0100 Subject: [PATCH 14/17] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 225ef49d..ab4f48d7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -260,7 +260,7 @@ "properties": { "vcf_spec": { "type": "string", - "description": "Specify a set of VCFs to produce with --vcf_spec \"REF[:LEN][,REF[:LEN]]*\".", + "description": "Specify a set of VCFs to produce with `--vcf_spec \"REF[:LEN][,REF[:LEN]]*\"`.", "help_text": "The paths matching `^REF` are used as a reference, while the sample haplotypes are derived from path names, e.g. when `DELIM=#` and with `-V chm13`, a path named HG002#1#ctg would be assigned to sample HG002 phase 1. If `LEN` is specified and greater than 0, the VCFs are decomposed, filtering sites whose max allele length is greater than `LEN`." } } From 3071e95b481be9ac4f09038dcde171328d8571e0 Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Thu, 14 Mar 2024 12:05:20 +0100 Subject: [PATCH 15/17] Update .github/workflows/linting.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 073e1876..cf9f0c85 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: From 57aa17387c415f8576c0720c1119784bd9bb684f Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 14 Mar 2024 12:09:10 +0100 Subject: [PATCH 16/17] revert liniting.yml review suggestion --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index cf9f0c85..073e1876 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: From 5daf69e995f498b7cd064cd499beb310c6bcb350 Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Thu, 14 Mar 2024 12:11:40 +0100 Subject: [PATCH 17/17] Update .github/workflows/download_pipeline.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 08622fd5..f361db64 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: