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feat: update samtools stats module with version topic support #9329

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feat: update samtools stats module with version topic support #9329

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@mribeirodantas mribeirodantas commented Nov 1, 2025 •
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  • Adds version topic channel to SAMTOOLS_STATS

PR checklist

Closes #9326

  • 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

ninaxiong11 and others added 9 commits October 29, 2025 16:01
@ninaxiong11
Update module: propr/propd (#9296)
1c8c773 
* Update module: propr/propd

* Update snapshots for abundance_differential_filter propd tests
@eduard-watchmaker @vagkaratzas
New align dedup bwamem (#9197)
b25dc59 
* tests

* tests

* confs

* confs

* confs

* confs

* confs

* confs

* confs

* gpu

* gpu

* last snap

* snap

* rm snap

* removed snapshot

* new snap

* lint

* lint

* channel

* channel

* channel

* snap test

* last snapshot

* last lint

* gpu snap

* PR feedback

* samtools sort prefix

* samtools sort prefix

* samtools sort prefix

* samtools sort prefix

* samtools sort prefix

* samtools sort prefix

* new snap

* new snap

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml

Co-authored-by: Evangelos Karatzas <[email protected]>

* changed tests again

* new cpu snapshot

* low memory to fq2bam

* conf revert

* rm nftest utils line and add lowmem to fq2bam

* revert lowmem to fq2bam

* index file

* path to index

* path to index

* revert nft utils

* test

* test

* removed parabricks

* new snapshot

* revert test data fw2bam

* revert test data fw2bam

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* Update subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <[email protected]>

* added new tag at test

* added new tag at test

* new snapshot

---------

Co-authored-by: root <[email protected]>
Co-authored-by: root <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
@Baksic-Ivan
Fastq decontaminate deacon (#9302)
73da03c 
* inital template

* first version

* review update
@maxulysse
update meta.yml and precommit hook version (#9313)
59a5cb7
@mashehu
renovate: group infra updates into separate PR and have a shorter sch…
5cd94fe 
…edule cycle (#9314)

group infra updates into separate PR and have a shorter schedule cycle
@renovate
chore(config): migrate renovate config (#9315)
84242c2 
Migrate config .github/renovate.json5

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@maxulysse
fix tuple for createsomaticpanelofnormals in the create som pon subwo…
6baf1c4 
…rkflow (#9322)

* fix tuple for createsomaticpanelofnormals

* realign
@JoseEspinosa @atrigila
Add stub to picard/mergesamfiles module (#9321)
2d74c66 
* Add stub to picard/mergesamfiles module

* Remove leaked file

* Update modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap

Co-authored-by: Anabella Trigila <[email protected]>

* Update modules/nf-core/picard/mergesamfiles/tests/main.nf.test

Co-authored-by: Anabella Trigila <[email protected]>

---------

Co-authored-by: Anabella Trigila <[email protected]>
@mribeirodantas
Adds version topic channel to SAMTOOLS_STATS
2118331
@mribeirodantas mribeirodantas self-assigned this Nov 1, 2025
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@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@mribeirodantas @ninaxiong11 @eduard-watchmaker @Baksic-Ivan @maxulysse @mashehu @JoseEspinosa