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Add failsafe options for Nextflow join operator #957

Merged
merged 11 commits into from
Mar 2, 2023
Merged

Add failsafe options for Nextflow join operator #957

merged 11 commits into from
Mar 2, 2023

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maxulysse
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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).

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github-actions bot commented Mar 2, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 59b3d0d

+| ✅ 152 tests passed       |+
#| ❔   8 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-02 15:31:44

FriederikeHanssen
FriederikeHanssen approved these changes Mar 2, 2023
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@FriederikeHanssen FriederikeHanssen left a comment

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looks good. I can test it on some larger data early next week. But if anyone else already has something they want to test in the meantime, i.e. we can merge already @BrunoGrandePhD.

It won't fix anything, but it might give us more insights on whats happening

@FriederikeHanssen
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did you run the manual mutect tests?

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did you run the manual mutect tests?

I did, and no issues there

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love it

@maxulysse maxulysse changed the title Add failsafe options for join operator in mutect2 subworkflows Add failsafe options for join operator Mar 2, 2023
@maxulysse maxulysse changed the title Add failsafe options for join operator Add failsafe options for Nextflow join operator Mar 2, 2023
@maxulysse maxulysse merged commit b2a8891 into nf-core:dev Mar 2, 2023
@maxulysse maxulysse deleted the mutect2 branch February 19, 2024 14:42
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen