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Fix empty barrnap output #553

Merged
merged 6 commits into from
Mar 14, 2023
Merged

Fix empty barrnap output #553

merged 6 commits into from
Mar 14, 2023

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jtangrot
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Fix so empty output from barrnap can be handled by sbdi_export, added warnings and error messages id barrnap fails to find rRNA sequences. This adresses #552

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/ampliseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
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github-actions bot commented Mar 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 36d1b55

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-14 07:46:52

d4straub
d4straub approved these changes Mar 13, 2023
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Looks good to me. test_iontorrent now produces a warning that no rRNA were identified.

@jtangrot
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Looks good to me. test_iontorrent now produces a warning that no rRNA were identified.

Yes, that's expected as those sequences are ITS2 only, so they are not recognized by barrnap. Do you think we should change the wording in the warning in some way?

@d4straub
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Do you think we should change the wording in the warning in some way?

Hm, in the warning "Barrnap could not identify any rRNA in the ASV sequences, which seem to be non-ribosomal. We recommended to use the --skip_barrnap option for these sequences." maybe , which seem to be non-ribosomal could be omitted? But thats not critical to me, just a thought. The error is fine I think.

@jtangrot
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Changed the wording as suggested. Thanks for approving!

@jtangrot jtangrot merged commit 6bc08cf into nf-core:dev Mar 14, 2023
@jtangrot jtangrot deleted the issue552 branch March 14, 2023 09:05
@jtangrot jtangrot mentioned this pull request Mar 16, 2023
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