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Add tests to VCF_COLLECT module#725

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delfiterradas wants to merge 15 commits intonf-core:devfrom
delfiterradas:vcf_collect
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Add tests to VCF_COLLECT module#725
delfiterradas wants to merge 15 commits intonf-core:devfrom
delfiterradas:vcf_collect

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@delfiterradas delfiterradas commented Jul 24, 2025

Closes #529

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
  • If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 24, 2025 •
edited by nf-core-bot
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Jul 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9867ac0

+| ✅ 293 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ stringtie_gtf = ch_stringtie_gtf.ifEmpty(null) // channel: [meta, gtf]
    _
  • schema_lint - Input mimetype is missing or empty
  • local_component_structure - fusioninspector_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: tests/default.nf.test
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-08-11 18:58:14

@delfiterradas delfiterradas changed the base branch from master to dev July 24, 2025 13:56
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rannick commented Jul 30, 2025 •
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Let's test with #726

atrigila
atrigila reviewed Aug 1, 2025
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While we wait for #726 to be merged, here are some suggestions that you could apply.

modules/local/vcf_collect/tests/main.nf.test
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@atrigila atrigila Aug 1, 2025

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Great job on setting up this test and making it work :) One thing that could improve this test is to directly use the final files from FUSIONINSPECTOR.out.abridged_tsv, AGAT_CONVERTSPGFF2TSV.out.tsv directly in the module (by uploading them to rnafusion/test-datasets first). This means that this test will be faster as you won't have to run STARFUSION_BUILD and FUSIONINSPECTOR or FUSIONREPORT_DETECT in the setup. You also won't have to use any extra params in this test.

I'd also like to highlight that your test is well designed and tests a few modules, so I think that with minimal modifications you can take this working structure and use it for testing the subworkflow: #729

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You can run the full test (in a cluster) and use the files that are created upstream of VCF_COLLECT to upload them to test-datasets. See an example working command in my comment here: #717 (review)

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@rannick rannick Awaiting requested review from rannick rannick will be requested when the pull request is marked ready for review rannick is a code owner

@nvnieuwk nvnieuwk Awaiting requested review from nvnieuwk nvnieuwk will be requested when the pull request is marked ready for review nvnieuwk is a code owner

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Create nf-tests for "vcf_collect" module

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@delfiterradas @rannick @atrigila