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Fix join mismatch error for joint tumor only Mutect2 #1181

Merged
merged 12 commits into from
Aug 31, 2023
Merged

Fix join mismatch error for joint tumor only Mutect2 #1181

merged 12 commits into from
Aug 31, 2023

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berguner
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Fixes the sporadic Join mismatch error by removing unnecessary metadata in tumor only mutect2 subworkflow.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented Aug 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4c1eced

+| ✅ 149 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-31 12:47:07

FriederikeHanssen
FriederikeHanssen reviewed Aug 16, 2023
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maxulysse
maxulysse approved these changes Aug 31, 2023
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LGTM

maxulysse
maxulysse reviewed Aug 31, 2023
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adamrtalbot
adamrtalbot reviewed Aug 31, 2023
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I haven't used subMap very much but from what I can tell this looks good. I've got some comments about code styling which might make it easier for the next person.

subworkflows/local/bam_variant_calling_somatic_all/main.nf Show resolved Hide resolved
subworkflows/local/bam_variant_calling_tumor_only_all/main.nf Show resolved Hide resolved
subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf Show resolved Hide resolved
asp8200
asp8200 approved these changes Aug 31, 2023
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Tests passing 🥳

@maxulysse maxulysse merged commit d4fa068 into nf-core:dev Aug 31, 2023
22 checks passed
@maxulysse maxulysse deleted the fix_join_mismatch branch August 31, 2023 13:24
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@adamrtalbot adamrtalbot adamrtalbot left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@maxulysse maxulysse maxulysse approved these changes

@asp8200 asp8200 asp8200 approved these changes

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@berguner @maxulysse @FriederikeHanssen @adamrtalbot @asp8200