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Refactor #1151

Merged
merged 22 commits into from
Jul 12, 2023
Merged

Refactor #1151

merged 22 commits into from
Jul 12, 2023

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FriederikeHanssen
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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 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).

@maxulysse
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Replace #1150

maxulysse
maxulysse reviewed Jul 11, 2023
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maxulysse
maxulysse reviewed Jul 11, 2023
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FriederikeHanssen
FriederikeHanssen commented Jul 11, 2023
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github-actions bot commented Jul 11, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit bf43387

+| ✅ 152 tests passed       |+
#| ❔   9 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-12 07:44:33

maxulysse
maxulysse reviewed Jul 12, 2023
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maxulysse
maxulysse approved these changes Jul 12, 2023
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Perfect

asp8200
asp8200 reviewed Jul 12, 2023
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conf/modules/sentieon_haplotyper.config
path: { "${params.outdir}/variant_calling/sentieon_haplotyper/${meta.id}/"},
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
if (params.tools && params.tools.contains('sentieon_haplotyper')) {
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@asp8200 asp8200 Jul 12, 2023 •
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Is the if-clause added to avoid the standard WARN when BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES doesn't run?

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yes

asp8200
asp8200 reviewed Jul 12, 2023
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conf/test/cache.config
@@ -63,6 +63,7 @@ process {
ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
}

// This must contain .* in order to properly overwrite the standard config in test cases
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I appreciate the comment 👍

asp8200
asp8200 approved these changes Jul 12, 2023
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Well done 👏

@FriederikeHanssen FriederikeHanssen merged commit ebd97a9 into dev Jul 12, 2023
@FriederikeHanssen FriederikeHanssen deleted the refactor branch July 12, 2023 12:06
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@asp8200 asp8200 asp8200 approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse @asp8200