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investigate haplotypecaller failuer on 3.7.0 #2069

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Merged
FriederikeHanssen merged 7 commits into from
Dec 10, 2025
Merged

investigate haplotypecaller failuer on 3.7.0 #2069

FriederikeHanssen merged 7 commits into from
Dec 10, 2025
+158 −109

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@FriederikeHanssen FriederikeHanssen commented Dec 8, 2025 •
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waiting on #2067

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).

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github-actions bot commented Dec 8, 2025

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @FriederikeHanssen,

It looks like this pull-request is has been made against the nf-core/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Dec 8, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 15d9356

+| ✅ 224 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-10 09:40:38

@FriederikeHanssen FriederikeHanssen changed the base branch from master to dev December 10, 2025 08:58
@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review December 10, 2025 09:10
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FriederikeHanssen commented Dec 10, 2025

Fixes a previously occuring bug on joining vcfs and tbis on haplotypecaller (and haplotyper): https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/OHPqhd7cPdLPS/v2/tasks

@FriederikeHanssen FriederikeHanssen merged commit c908b84 into dev Dec 10, 2025
72 of 74 checks passed
@FriederikeHanssen FriederikeHanssen mentioned this pull request Dec 11, 2025
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