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New module: picard/splitsambynumberofreads #8679

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New module: picard/splitsambynumberofreads #8679

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@Y-Pei Y-Pei commented Jun 19, 2025 •
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PR checklist

Closes #8669

  • 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
  • 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

@Y-Pei Y-Pei marked this pull request as draft June 19, 2025 15:47
@Y-Pei Y-Pei self-assigned this Jun 19, 2025
@Y-Pei Y-Pei added the new module Adding a new module label Jun 20, 2025
@Y-Pei Y-Pei marked this pull request as ready for review June 20, 2025 15:46
@Y-Pei Y-Pei requested a review from pinin4fjords as a code owner June 20, 2025 15:46
@Y-Pei Y-Pei force-pushed the picard_splitsamBynumberofreads branch from 1cbd72f to 0dcbc76 Compare June 20, 2025 15:47
SPPearce
SPPearce requested changes Jun 22, 2025
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Also, can the tool work on cram files?

@Y-Pei Y-Pei marked this pull request as draft June 23, 2025 07:42
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Y-Pei commented Jun 23, 2025

Many thanks for the review and suggestions! All requested changes updated. Re-review please?

@Y-Pei Y-Pei requested a review from SPPearce June 23, 2025 15:33
@Y-Pei Y-Pei marked this pull request as ready for review June 24, 2025 08:02
SPPearce
SPPearce reviewed Jun 29, 2025
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Sorry, missed the request for re-review
Does the tool use the fasta index, normally cram files just take the fasta itself

@Y-Pei Y-Pei marked this pull request as draft June 30, 2025 09:39
Y-Pei and others added 11 commits June 30, 2025 14:22
@Y-Pei
update branch
8008157
@Y-Pei
linted and fixed meta.yml
42cc634
@Y-Pei
added conda test. added more detail to meta.
9df8f5f
@Y-Pei
updated tests
890c682
@Y-Pei
fixed failing conda test with updated picard version
4189790
@Y-Pei
bug fixed causing conda test to fail - verioning lined updated to gen…
d40c095 
…erate consistent versions for picard in both conda and singularity.
@Y-Pei @SPPearce
Update modules/nf-core/picard/splitsambynumberofreads/main.nf
ca6860c 
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
@Y-Pei
restore .pre-commit-config.yaml
7ab53ca
@Y-Pei
Stub now makes N files in split-by-N-file mode. Updated test to use s…
0baff5c 
…maller split_to_N_reads to generate more output files. Added support for crams. Updated meta.yml. Regernerated test snaps accordingly.
@Y-Pei @SPPearce
Apply suggestions from code review
166b3a7 
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
@Y-Pei
Using <input> intead of <bam> in the input block. updated main and me…
8acbd7d 
…ta accordingly.
@Y-Pei Y-Pei force-pushed the picard_splitsamBynumberofreads branch from 265c281 to 8acbd7d Compare June 30, 2025 13:22
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Y-Pei commented Jun 30, 2025

Does the tool use the fasta index, normally cram files just take the fasta itself

Yes seems like fai is required - would fail without

@Y-Pei Y-Pei marked this pull request as ready for review June 30, 2025 13:35
@Y-Pei Y-Pei requested a review from SPPearce June 30, 2025 13:36
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@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

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new module: PICARD/SPLITSAMBYNUMBEROFREADS
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