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Update samtools #74

Merged
merged 7 commits into from
Feb 14, 2024
Merged

Update samtools #74

merged 7 commits into from
Feb 14, 2024

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asp8200
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@asp8200 asp8200 commented Feb 13, 2024 •
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Update samtools to v1.19.2.

Had to do some search-replace of fasta to fasta.map{ it -> [[:], it] } in calls to samtools-models. There might be a more elegant solution though.

Detail: I got this warning: WARN: Undocumented setting "docker.userEmulation" is not supported any more - please remove it from your config so I removed docker.userEmulation from nextflow.config.

TO-DO: Update CHANGELOG.

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github-actions bot commented Feb 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8d238d5

+| ✅ 170 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.0
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in WorkflowBamtofastq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-13 22:52:50

maxulysse
maxulysse reviewed Feb 13, 2024
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looking good, but you'll need to sync your branch with dev now that we merged the TEMPLATE sync

@maxulysse maxulysse merged commit 3122b17 into nf-core:dev Feb 14, 2024
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asp8200 commented Feb 14, 2024

Thanks for merging. What about the changelog?

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@maxulysse maxulysse maxulysse approved these changes

@SusiJo SusiJo Awaiting requested review from SusiJo

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

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@asp8200 @maxulysse