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Add cleanup steps to Metagenomics db build tools (Kaiju, KrakenUniq) #7317

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merged 16 commits into from
Jan 17, 2025

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@jfy133 jfy133 commented Jan 16, 2025

Almost there, but KRAKENUNIQ_BUILD exports a directory, and inside that there are three variable files (database.report.tsv, timestamp, and database-build.log)

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

@jfy133 jfy133 changed the title Metagenomics db build cleanup Add cleanup steps to Metagenomics db build tools (Kaiju, KrakenUniq) Jan 17, 2025
@jfy133 jfy133 marked this pull request as ready for review January 17, 2025 07:40
@jfy133 jfy133 requested a review from a team as a code owner January 17, 2025 07:40
@sateeshperi sateeshperi added this pull request to the merge queue Jan 17, 2025
Merged via the queue into nf-core:master with commit f1304d4 Jan 17, 2025
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2 participants