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Investigating potential mutect2 filter bug

Open maxulysse opened this issue 1 month ago • 2 comments

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/sarek branch on the 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 <OUTDIR>).
  • [ ] 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).

maxulysse avatar Nov 27 '25 10:11 maxulysse

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2. 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.

nf-core-bot avatar Nov 27 '25 10:11 nf-core-bot

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit f2fad7d

+| ✅ 228 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-11-27 13:10:59

github-actions[bot] avatar Nov 27 '25 10:11 github-actions[bot]