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feat: update samtools stats module with version topic support #9330

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Merged
merged 11 commits into from
Nov 4, 2025
Merged

feat: update samtools stats module with version topic support #9330

merged 11 commits into from
Nov 4, 2025
+177 −199

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@mribeirodantas
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@mribeirodantas mribeirodantas commented Nov 1, 2025 •
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PR checklist

Closes #9326

There were missing version channel mixings from the SAMTOOLS SORT that are fixed in this PR.

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@mribeirodantas mribeirodantas self-assigned this Nov 1, 2025
@mribeirodantas mribeirodantas changed the base branch from topics-adoption to master November 1, 2025 05:12
@mribeirodantas mribeirodantas changed the base branch from master to topics-adoption November 1, 2025 05:13
@mribeirodantas mribeirodantas linked an issue Nov 1, 2025 that may be closed by this pull request
update module: SAMTOOLS_STATS - add version topic #9326
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@mribeirodantas mribeirodantas force-pushed the addtopicversion_samtoolsstats branch from f3dff13 to 6ada243 Compare November 1, 2025 05:51
@mribeirodantas mribeirodantas changed the base branch from topics-adoption to master November 1, 2025 06:25
@mribeirodantas mribeirodantas changed the base branch from master to topics-adoption November 1, 2025 06:29
SPPearce
SPPearce reviewed Nov 1, 2025
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@mribeirodantas mribeirodantas force-pushed the addtopicversion_samtoolsstats branch from dc4792e to f0895e3 Compare November 3, 2025 03:17
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mribeirodantas commented Nov 3, 2025

The only nf tests failing are those that require GPU and I don't have GPUs to test 😓 Anyone knows an easy way to make the GitHub Action tests run in this branch for this PR specifically? @nvnieuwk @SPPearce @maxulysse

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mashehu commented Nov 3, 2025

@nf-core-bot update gpu snapshot path: modules/nf-core/parabricks/fq2bammeth

@nf-core-bot nf-core-bot requested review from a team as code owners November 3, 2025 09:07
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mashehu commented Nov 3, 2025

okay, that didn't work as expected...

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mashehu commented Nov 3, 2025

@nf-core-bot update gpu snapshot path: subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap

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mashehu commented Nov 3, 2025

@nf-core-bot update gpu snapshot path: subworkflows/nf-core/fastq_align_dedup_bwameth

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mribeirodantas commented Nov 3, 2025

LGTM?

@SPPearce SPPearce merged commit 6d4873b into topics-adoption Nov 4, 2025
@SPPearce SPPearce deleted the addtopicversion_samtoolsstats branch November 4, 2025 08:28
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@SPPearce SPPearce SPPearce approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

@nvnieuwk nvnieuwk Awaiting requested review from nvnieuwk

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update module: SAMTOOLS_STATS - add version topic

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