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Add a Find/Concatenate module #7356

Merged
merged 10 commits into from
Jan 27, 2025
Merged

Add a Find/Concatenate module #7356

merged 10 commits into from
Jan 27, 2025

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BioWilko
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@BioWilko BioWilko commented Jan 23, 2025

This module is HEAVILY based on the CAT/CAT module, the difference being that it uses find to concatenate files iteratively therefore avoiding wildcard expansion, this allows any number of files to be concatenated since it doesn't run into the argument limit.

PR checklist

  • 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 self-requested a review January 24, 2025 04:48
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I've updated the meta for you, left one comment but I think it's OK assuming tests pass - I would like to get second pair of eyes though

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I think other than removing the maybe unnecessary commented out test assertions we are good to go?

modules/nf-core/find/concatenate/tests/main.nf.test Outdated Show resolved Hide resolved
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modules/nf-core/find/concatenate/tests/main.nf.test Outdated Show resolved Hide resolved
@BioWilko BioWilko enabled auto-merge January 27, 2025 08:52
@BioWilko BioWilko added this pull request to the merge queue Jan 27, 2025
@BioWilko BioWilko removed this pull request from the merge queue due to a manual request Jan 27, 2025
@BioWilko BioWilko enabled auto-merge January 27, 2025 10:43
@BioWilko BioWilko added this pull request to the merge queue Jan 27, 2025
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Jan 27, 2025
@BioWilko BioWilko added this pull request to the merge queue Jan 27, 2025
Merged via the queue into nf-core:master with commit 326bde8 Jan 27, 2025
27 of 32 checks passed
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3 participants