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Add check agianst incompatible odb12 files., and improve docs descrip… #790

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@jfy133 jfy133 commented Apr 9, 2025

closes #775

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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Apr 9, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bb4ccc8

+| ✅ 334 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  52 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-04-10 06:56:42

@jfy133 jfy133 mentioned this pull request Apr 9, 2025
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prototaxites
prototaxites reviewed Apr 10, 2025
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subworkflows/local/utils_nfcore_mag_pipeline/main.nf
@@ -307,6 +307,10 @@ def validateInputParameters(hybrid) {
log.warn('[nf-core/mag]: --skip_binqc is specified, but --skip_gtdbtk is explictly set to run! GTDB-tk will be omitted because GTDB-tk bin classification requires bin filtering based on BUSCO or CheckM QC results to avoid GTDB-tk errors.')
}

if (params.busco_db && params.busco_db.contains('_odb12.')) {
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Can this go in the "pattern:" section of the nextflow_schema.json with a helpful error message?

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https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/#pattern

https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/#errormessage

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Ah good idea

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Note: this is unnecessary once the BUSCO update PR is in

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jfy133 commented Apr 15, 2025

OK, will close and any docs can be copied over

@jfy133 jfy133 closed this Apr 15, 2025
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