Fix empty barrnap output

jtangrot commented 1 year ago

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

[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
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github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 36d1b55

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

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jtangrot commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Changed the wording as suggested. Thanks for approving!

nf-core / ampliseq