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Update BUSCO module #7199

Merged
merged 8 commits into from
Dec 11, 2024
Merged

Update BUSCO module #7199

merged 8 commits into from
Dec 11, 2024

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dialvarezs
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@dialvarezs dialvarezs commented Dec 11, 2024

Description

This PR:

  • Updates BUSCO to the most recent version (v5.8.2)
  • Updates tests to use OrthoDB v12
  • Adds auto_prok and auto_euk as lineage options to enable --auto-lineage-prok and --auto-lineage-euk, respectively.

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 mentioned this pull request Dec 11, 2024
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@jfy133
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jfy133 commented Dec 11, 2024

@dialvarezs linting should pass, I suspect the second test(s0 will fail due to this md5sum mismatch:

      "test-bacteria_odb12-busco.batch_summary.txt:md5,c8a18a22e2d290e159292a120990d862",		   |	    "test-bacteria_odb12-busco.batch_summary.txt:md5,e9b28bb5f3f605dea87b52880f51635a",
      ```
      
      So you may need to change the nf-test assertion for this

@dialvarezs
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Yes, I don't know why GitHub is getting a different checksum. I have run that test multiple times in my machine with docker and apptainer and I get the same checkmsum everytime lol

@dialvarezs dialvarezs added this pull request to the merge queue Dec 11, 2024
Merged via the queue into nf-core:master with commit abd32eb Dec 11, 2024
33 checks passed
@dialvarezs dialvarezs deleted the update-busco branch December 11, 2024 20:43
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2 participants