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@LouisLeNezet LouisLeNezet commented Nov 25, 2025

PR checklist

Add region to minimac command for parallelization purpose
Add minimac imputation subworkflow for vcf files.

  • 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

@LouisLeNezet LouisLeNezet marked this pull request as ready for review November 25, 2025 09:15
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@famosab famosab left a comment

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Nice work!

@LouisLeNezet LouisLeNezet added this pull request to the merge queue Dec 11, 2025
Merged via the queue into nf-core:master with commit 9a571f1 Dec 11, 2025
342 of 382 checks passed
@LouisLeNezet LouisLeNezet deleted the vcf_impute_minimac4 branch December 11, 2025 17:38
vagkaratzas pushed a commit that referenced this pull request Dec 12, 2025
* Add vcf_impute_minimac4

* Update linting

* Update test

* Fix linting

* Update minimac4 sbwf

* Remove tag

* Remove tag

* Fix linting

* Add comment

* Update snapshot

* Fix nf-test
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3 participants