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Fix gtdb dirrectory input #583

Merged
merged 5 commits into from
Feb 12, 2024
Merged

Fix gtdb dirrectory input #583

merged 5 commits into from
Feb 12, 2024

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jfy133
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@jfy133 jfy133 commented Feb 12, 2024

I discovered when testing that supplying an already unpacked GTDB directory, this would fail at the CLASSIFYWF module, as this module doesn't expect the directory, but rather a list of the contents itself. I'm not sure why this is....

I will in the future update the module (And thoroughly test it), but for now this workaround makes the module work for directory input.

The PR also includes setting a GTDBTK contamination filter to 0, so when it is tested manually (as it the database doesn't fit on GHA), we can be sure the module executes.

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 lint).
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jfy133
jfy133 commented Feb 12, 2024
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github-actions bot commented Feb 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d18108f

+| ✅ 211 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-12 16:24:11

CarsonJM
CarsonJM approved these changes Feb 12, 2024
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Thanks for the comment explaining the rationale behind the fix!

@jfy133 jfy133 merged commit f21bcf5 into dev Feb 12, 2024
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@jfy133 jfy133 deleted the fix-gtdbtk-dir-input branch February 12, 2024 16:28
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@CarsonJM CarsonJM CarsonJM approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@jfy133 @FriederikeHanssen @CarsonJM