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Add metamaps/classify #5466

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@sofstam sofstam commented Apr 11, 2024

PR checklist

Closes the secode module for #1403

  • 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

@sofstam sofstam marked this pull request as ready for review May 16, 2024 08:43
@sofstam sofstam requested a review from a team as a code owner May 16, 2024 08:43
@sofstam sofstam requested review from kpadm and removed request for a team May 16, 2024 08:43
modules/nf-core/metamaps/classify/main.nf Outdated Show resolved Hide resolved
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Looking very good! Can you update the meta.yaml too?

@jfy133 jfy133 self-requested a review May 16, 2024 09:42
Comment on lines +36 to +38
input[1] = UNTAR.out.untar.map { id, it ->
filename = it.toString() + "/DB.fa"
return [ file(filename) ]
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It would be better to use find within the module to pick up this file, rather than trying to hardcode a path, with this you srr converting s psth to a.string which isnt ideal

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sofstam commented May 16, 2024

@nvnieuwk Updated the meta.yaml

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Thank you! I'll approve once you've addressed James' suggestion :p

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sofstam commented May 16, 2024

Working on this now :D

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