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CheckM2 module updates #7259

Merged
merged 4 commits into from
Dec 31, 2024
Merged

CheckM2 module updates #7259

merged 4 commits into from
Dec 31, 2024

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dialvarezs
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@dialvarezs dialvarezs commented Dec 21, 2024

This PR introduces a few changes to the CheckM2 modules:

  • Creates a copy of the main output of checkm2/predict to prevent clashing when gathering multiple of these files.
  • Updates the test data to use a bacterial genome.
  • Place groovy.json.JsonSlurper directly in checkm2/databasedownload to fix an error reported by the language server.

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

@dialvarezs dialvarezs enabled auto-merge December 23, 2024 16:26
@dialvarezs dialvarezs disabled auto-merge December 23, 2024 23:17
@dialvarezs
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dialvarezs commented Dec 27, 2024

Proof that test is passing with local Docker:
Is it possible to get a forced merge for this PR?

image

@SPPearce SPPearce merged commit ad43b5d into nf-core:master Dec 31, 2024
50 of 56 checks passed
@SPPearce
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I was about to say that I don't have the power to force merge, but apparently I do now!

@dialvarezs
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Thanks!

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2 participants