removed the option of initializing the pipeline with samplesheet and network parameter #184
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Schansiate wants to merge 7 commits into
Open
removed the option of initializing the pipeline with samplesheet and network parameter #184Schansiate wants to merge 7 commits into
Schansiate wants to merge 7 commits into
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added 2 commits
May 12, 2026 23:20
…seed/network parameter to only accepting samplesheet or seed and network parameter
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Pull request overview
This PR updates pipeline initialisation logic to enforce mutually exclusive input modes (either a samplesheet or explicit --seeds + --network), and also adjusts repository CI/docs files.
Changes:
- Enforce an error when
--inputis used together with--seedsand/or--network, and simplify channel creation from the samplesheet. - Modify GitHub Actions linting workflows (pre-commit + nf-core lint installation/branch conditions).
- Update contributor-facing docs/templates and ignore patterns.
Reviewed changes
Copilot reviewed 7 out of 11 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline/main.nf |
Enforces exclusive initialisation mode and simplifies samplesheet-derived channels. |
ro-crate-metadata.json |
Minor documentation/formatting update in embedded description content. |
docs/CONTRIBUTING.md |
Replaces prior contributing guidelines with a tool-integration checklist (plus a minor command reference). |
.prettierignore |
Adds additional JSON filenames to ignore list. |
.github/workflows/linting.yml |
Reworks pre-commit execution and nf-core lint installation; changes branch gating logic. |
.github/workflows/linting_comment.yml |
Updates action versions used to fetch artifacts and post sticky PR comments. |
.github/workflows/branch.yml |
Updates the action version used to add PR comments on branch protection failures. |
.github/PULL_REQUEST_TEMPLATE.md |
Updates CONTRIBUTING links (currently pointing to a non-existent path/branch). |
Comments suppressed due to low confidence (1)
.github/PULL_REQUEST_TEMPLATE.md:19
- The PR checklist item links to
tree/master/.github/CONTRIBUTING.md, which does not exist in this repo. Update this URL to the correct CONTRIBUTING location so the checklist remains actionable.
- [ ] 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/diseasemodulediscovery/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/diseasemodulediscovery _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 | ||
| uses: nf-core/setup-nextflow@v2 |
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| - name: Run nf-core pipelines lint | ||
| if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} | ||
| 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 | ||
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| - name: Run nf-core pipelines lint --release | ||
| if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }} | ||
| if: ${{ github.base_ref == 'master' }} | ||
| env: |
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| Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. | ||
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| Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/diseasemodulediscovery/tree/main/docs/CONTRIBUTING.md) | ||
| Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/diseasemodulediscovery/tree/master/.github/CONTRIBUTING.md) | ||
| --> |
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| # Including a new active module detection tool | ||
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| 1. Create a new branch for your tool. | ||
| 2. Add a function to the bin/graph_tool_parser.py script for preparing the tool-specific network input format. The script is built around the [graph-tool](https://graph-tool.skewed.de/) Python package. An example is the safe_diamond() function, which saves a simple edge list in CSV format. Add the function as an option in the save() function and a command line option for `--format` in parse_args(). The output file name has to include the option specified with `--format` since nextflow uses this pattern to check whether the output file was successfully generated. The script expects a .gt file as input. Run the pipeline with the "test" profile to generate a .gt example file in `<OUTDIR>/graphtoolparser`, which you can use to test the parsing function by executing the parsing script directly via the command line. | ||
| 3. Create a module for the tool. (Example with comments: `modules/local/diamond/main.nf` and `modules/local/domino/`) | ||
| 4. Create a subworkflow wrapping the tool together with the input parser. (Example with comments: `subworkflows/local/gt_diamond/main.nf` and `subworkflows/local/gt_domino/main.nf`) |
| 5. Include the subworkflow in the `workflows/modulediscovery.nf` file. Again, DIAMOnD and DOMINO are included as examples. | ||
| 6. Test checks locally: | ||
| 1. Run tests via, e.g., `nextflow run main.nf -profile singularity,test --outdir results`. | ||
| 2. Run `nf-core lint`. |
added 4 commits
May 13, 2026 11:43
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changed pipeline initialization to accept sample sheet only or seed and network files as parameters
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).