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Merged
georgiakes merged 10 commits into from
Dec 10, 2025
Merged

Add module picard/collectvariantcallingmetrics #9502

georgiakes merged 10 commits into from
Dec 10, 2025

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@georgiakes georgiakes commented Dec 4, 2025

PR checklist

Closes #9501

  • [] 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

@georgiakes georgiakes added new module Adding a new module Ready for Review labels Dec 4, 2025
@georgiakes georgiakes requested a review from famosab December 5, 2025 14:52
famosab
famosab reviewed Dec 8, 2025
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Just a few small things :)

@georgiakes georgiakes force-pushed the add-picard-collectvariantcallingmetrics branch from 742c16f to e3b7f3b Compare December 10, 2025 13:02
famosab
famosab approved these changes Dec 10, 2025
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Nice work, I would just remove the TODO statement :)

@georgiakes georgiakes force-pushed the add-picard-collectvariantcallingmetrics branch from f3be96e to aa5ef76 Compare December 10, 2025 14:09
@georgiakes georgiakes enabled auto-merge December 10, 2025 14:11
@georgiakes georgiakes added this pull request to the merge queue Dec 10, 2025
Merged via the queue into nf-core:master with commit d6672e7 Dec 10, 2025
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@georgiakes georgiakes deleted the add-picard-collectvariantcallingmetrics branch December 10, 2025 14:15
vagkaratzas pushed a commit that referenced this pull request Dec 12, 2025
@georgiakes @famosab @vagkaratzas
Add module picard/collectvariantcallingmetrics (#9502)
7a6165f 
* Add module picard/collectvariantcallingmetrics

* Run prettier

* Fix format

* Make one input  tuple

* Change test input structure

* Add md5 checksum

* Update snapshot

* Update meta.yml

* Support multithreading

* Remove TODO

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

---------

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
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new module: PICARD/COLLECTVARIANTCALLINGMETRICS

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@georgiakes @famosab