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Update gatk4 mutect2 to add --alleles parameter for force calling#9020

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maxulysse merged 7 commits into
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jchchiu:update-gatk4-mutect2
Sep 10, 2025
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Update gatk4 mutect2 to add --alleles parameter for force calling#9020
maxulysse merged 7 commits into
nf-core:masterfrom
jchchiu:update-gatk4-mutect2

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@jchchiu jchchiu commented Sep 8, 2025 •
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PR checklist

Closes #9019

  • 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

For Issue #9019 and nf-core/sarek#1952

@jchchiu jchchiu requested a review from maxulysse as a code owner September 8, 2025 23:06
maxulysse
maxulysse approved these changes Sep 9, 2025
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praise
Nice work

maxulysse
maxulysse reviewed Sep 9, 2025
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Comment thread modules/nf-core/gatk4/mutect2/main.nf Outdated
Comment on lines +17 to +20
path panel_of_normals
path panel_of_normals_tbi
path mutect2_force_call
path mutect2_force_call_tbi

@maxulysse maxulysse Sep 9, 2025

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how about we rename and reorder these inputs (just to keep a logic with the args from mutect2 and the names?

    path alleles
    path alleles_tbi
    path germline_resource
    path germline_resource_tbi
    path panel_of_normals
    path panel_of_normals_tbi

@maxulysse maxulysse Sep 9, 2025

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Reorder, because I like a list nicely ordered 😆

@jchchiu jchchiu requested a review from maxulysse September 10, 2025 04:45
@maxulysse maxulysse added this pull request to the merge queue Sep 10, 2025
Merged via the queue into nf-core:master with commit 3dbb6ed Sep 10, 2025
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@maxulysse maxulysse mentioned this pull request Sep 10, 2025
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chaochaowong pushed a commit to chaochaowong/modules that referenced this pull request Sep 30, 2025
@jchchiu @chaochaowong
Update gatk4 mutect2 to add --alleles parameter for force calling (nf…
67ca51c 
…-core#9020)

* Add mutect2 --alleles force call parameter

* update mutect2 tests

* update subworkflow tests

* fix formatting

* update mutect2 module to rename and reorder parameter

* update subworkflows to rename and reorder force call parameter
cavenel pushed a commit to cavenel/modules that referenced this pull request Feb 5, 2026
@jchchiu @cavenel
Update gatk4 mutect2 to add --alleles parameter for force calling (nf…
eaf3de6 
…-core#9020)

* Add mutect2 --alleles force call parameter

* update mutect2 tests

* update subworkflow tests

* fix formatting

* update mutect2 module to rename and reorder parameter

* update subworkflows to rename and reorder force call parameter
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update module: gatk4/mutect2

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