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Gvcf are published also when all intervals are processed at once #1172

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merged 4 commits into from
Aug 8, 2023
Merged

Gvcf are published also when all intervals are processed at once #1172

merged 4 commits into from
Aug 8, 2023

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FriederikeHanssen
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Close #764

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).

@FriederikeHanssen FriederikeHanssen mentioned this pull request Aug 4, 2023
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github-actions bot commented Aug 4, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a3bf92c

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-05 17:28:56

@asp8200
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asp8200 commented Aug 5, 2023

Looks fine. How about adding a test which covers the bug which this PR is fixing?

I think one could just extend tests/test_joint_germline.yml with

nextflow run main.nf -profile test_cache, --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results

(That is similar to the existing test, but with the profile targeted removed.)
and the check for the gvcf-files under results/variant_calling/haplotypecaller/testN and results/variant_calling/haplotypecaller/testT.

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asp8200 commented Aug 5, 2023 •
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I wonder if one should also remove the enabled: !params.joint_germline from the config of SENTIEON_HAPLOTYPER 🤔

sarek/conf/modules/sentieon_haplotyper.config

Line 22 in 12ae9e5

enabled: !params.joint_germline,

(And add a test for that as well.)

@FriederikeHanssen
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I wonder if one should also remove the enabled: !params.joint_germline from the config of SENTIEON_HAPLOTYPER 🤔

sarek/conf/modules/sentieon_haplotyper.config

Line 22 in 12ae9e5

enabled: !params.joint_germline,

(And add a test for that as well.)

sure but I would leave that up to a seaparate PR. the issue and the fix here are for haplotypecaller

@FriederikeHanssen FriederikeHanssen changed the title make gvcf are published also when all intervals are processed at once Gvcf are published also when all intervals are processed at once Aug 8, 2023
@FriederikeHanssen FriederikeHanssen merged commit 2ae0d45 into nf-core:dev Aug 8, 2023
@hangxue-wustl hangxue-wustl mentioned this pull request Jun 28, 2024
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@asp8200 asp8200 asp8200 approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@FriederikeHanssen @asp8200