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Update samtools and bcftools sub process for parallelization and add index files#10319

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LouisLeNezet merged 4 commits into
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LouisLeNezet:one_tuple
Mar 3, 2026
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Update samtools and bcftools sub process for parallelization and add index files#10319
LouisLeNezet merged 4 commits into
nf-core:masterfrom
LouisLeNezet:one_tuple

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@LouisLeNezet LouisLeNezet commented Mar 3, 2026

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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

@LouisLeNezet LouisLeNezet self-assigned this Mar 3, 2026
muffato
muffato reviewed Mar 3, 2026
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Comment thread modules/nf-core/bcftools/pluginsplit/main.nf
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@muffato muffato Mar 3, 2026

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I don't know bcftools/pluginsplit. Is it more natural / easier to have everything on one channel ?

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@LouisLeNezet LouisLeNezet Mar 3, 2026

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It is in my case, as I need to parallelise by samples and regions.

@LouisLeNezet LouisLeNezet requested a review from muffato March 3, 2026 18:12
@LouisLeNezet LouisLeNezet added this pull request to the merge queue Mar 3, 2026
github-merge-queue Bot pushed a commit that referenced this pull request Mar 3, 2026
@LouisLeNezet
Update samtools and bcftools sub process for parallelization and add …
440edf7 
…index files (#10319)

* Update modules

* Fix meta

* Update samtools stub
@LouisLeNezet LouisLeNezet added this pull request to the merge queue Mar 3, 2026
Merged via the queue into nf-core:master with commit 8c79e04 Mar 3, 2026
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@LouisLeNezet LouisLeNezet deleted the one_tuple branch March 3, 2026 19:07
dbaku42 pushed a commit to dbaku42/modules that referenced this pull request Apr 29, 2026
@LouisLeNezet @dbaku42
Update samtools and bcftools sub process for parallelization and add …
b9ae2dd 
…index files (nf-core#10319)

* Update modules

* Fix meta

* Update samtools stub
dbaku42 pushed a commit to dbaku42/modules that referenced this pull request Apr 29, 2026
@LouisLeNezet @dbaku42
Update samtools and bcftools sub process for parallelization and add …
577e1a6 
…index files (nf-core#10319)

* Update modules

* Fix meta

* Update samtools stub
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@muffato muffato muffato approved these changes

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