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Change gatk_vf params from integer to floats #144

Merged
merged 1 commit into from
Jun 17, 2024
Merged

Change gatk_vf params from integer to floats #144

merged 1 commit into from
Jun 17, 2024

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robsyme
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@robsyme robsyme commented Jun 17, 2024 •
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The default qd and fs filters in the nextflow schema are integers, even though the help text (correctly) identifies that these should be floats.

At the moment, the defaults are integers. These integers can end up in the pipeline which will cause the GATK VariantFilter to fail if the input data contains variants that have fractional values for FS or QD.

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/rnavar branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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 Jun 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 08240b5

+| ✅ 213 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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!

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-17 15:12:28

@maxulysse maxulysse merged commit 0b2c66e into dev Jun 17, 2024
12 checks passed
@maxulysse maxulysse deleted the filter-default-fix branch June 17, 2024 15:48
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@maxulysse maxulysse maxulysse approved these changes

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@robsyme @maxulysse