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Add CATPACK_PREPARE #7312

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Add CATPACK_PREPARE #7312

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@jfy133 jfy133 commented Jan 15, 2025

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 marked this pull request as ready for review January 17, 2025 09:02
@jfy133 jfy133 mentioned this pull request Jan 19, 2025
17 tasks
Comment on lines +25 to +26
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
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Suggested change
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

Comment on lines +44 to +45
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
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Suggested change
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"

Comment on lines +17 to +19
tuple val(meta), path("${prefix}/db/"), emit: db
tuple val(meta), path("${prefix}/tax/"), emit: taxonomy
path "versions.yml", emit: versions
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Suggested change
tuple val(meta), path("${prefix}/db/"), emit: db
tuple val(meta), path("${prefix}/tax/"), emit: taxonomy
path "versions.yml", emit: versions
tuple val(meta), path("${prefix}/db/") , emit: db
tuple val(meta), path("${prefix}/tax/") , emit: taxonomy
path "versions.yml" , emit: versions

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2 participants