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gatk4/selectvariants: Update documentation and module improvements #7907 #8121

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gatk4/selectvariants: Update documentation and module improvements #7907 #8121

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Alveen-o
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PR checklist

Closes #XXX

  • 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

@Alveen-o Alveen-o requested a review from maxulysse as a code owner March 26, 2025 15:02
@Alveen-o Alveen-o enabled auto-merge March 26, 2025 15:02
@Alveen-o Alveen-o self-assigned this Mar 26, 2025
famosab
famosab requested changes Mar 31, 2025
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@famosab famosab left a comment

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Thanks for your contribution! Please clean up this PR. A lot of files are not needed to work with module. Check out the other gatk4 modules :)

modules/nf-core/gatk4/selectvariants/main.nf
Comment on lines -16 to +21
path "versions.yml" , emit: versions
path "versions.yml", emit: versions
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Please leave as is :)

modules/nf-core/gatk4/selectvariants/main.nf
Comment on lines +13 to +15
path fasta
path fasta_fai
path dict
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Please pass them with metas

modules/nf-core/gatk4/selectvariants/main.nf
} else {
avail_mem = (task.memory.mega*0.8).intValue()
def interval_command = intervals ? "--intervals ${intervals}" : ""
def avail_mem = 3
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Why is this value hardcoded?

modules/nf-core/gatk4/selectvariants/main.nf
}

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Suggested change

modules/nf-core/gatk4/selectvariants/main.nf
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

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Suggested change

modules/nf-core/gatk4/selectvariants/tests/nextflow.config
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YOu should not neeed this here, please remove it.

modules/nf-core/gatk4/selectvariants/tests/modules.json
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YOu should not neeed this here, please remove it.

modules/nf-core/gatk4/selectvariants/tests/snapshots/main.nf.test.snap
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YOu should not neeed this here, please remove it.

modules/nf-core/gatk4/selectvariants/tests/test-data/test.vcf
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YOu should not neeed this here, please remove it.

modules/nf-core/gatk4/selectvariants/tests/test.yml
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YOu should not neeed this here, please remove it.

@famosab famosab disabled auto-merge March 31, 2025 11:37
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@famosab famosab famosab requested changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@Alveen-o @famosab