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POC Use of nfcore.utils for R templace#11933

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LouisLeNezet wants to merge 6 commits into
nf-core:masterfrom
LouisLeNezet:nfcore_utils
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POC Use of nfcore.utils for R templace#11933
LouisLeNezet wants to merge 6 commits into
nf-core:masterfrom
LouisLeNezet:nfcore_utils

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@LouisLeNezet

@LouisLeNezet LouisLeNezet commented Jun 9, 2026

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PR checklist

This PR is a Proof Of Concept for the use of the dedicated library nfcore.utils to manage input QC and versions creation.

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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 self-assigned this Jun 9, 2026
mashehu
mashehu reviewed Jun 9, 2026
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Comment thread modules/nf-core/custom/geneticmapconvert/main.nf Outdated
r-data.table: \$(Rscript -e "cat(as.character(packageVersion('data.table')))")
r-janitor: \$(Rscript -e "cat(as.character(packageVersion('janitor')))")
END_VERSIONS
Rscript -e "nfcore.utils::process_end(packages = list('r-data.table' = 'data.table', 'r-janitor' = 'janitor'), task_name = '${task.process}')"

@mashehu mashehu Jun 9, 2026

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I think the export file name "versions.yml" should also be added as an argument, to make it clearer what happens.

@LouisLeNezet LouisLeNezet Jun 9, 2026

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I could do that !
I will need to update the package.

@mashehu mashehu Jun 9, 2026

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and instead of process_end it could be called export_versions or so

@LouisLeNezet LouisLeNezet Jun 9, 2026 •
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process_end() also create the R_session.log

@LouisLeNezet LouisLeNezet requested a review from mashehu June 10, 2026 15:45
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@maxulysse maxulysse maxulysse approved these changes

@mashehu mashehu Awaiting requested review from mashehu

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@LouisLeNezet @maxulysse @mashehu