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Update summarize_barrnap.py #722

Merged
merged 4 commits into from
Mar 26, 2024
Merged

Update summarize_barrnap.py #722

merged 4 commits into from
Mar 26, 2024

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vaulot
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@vaulot vaulot commented Mar 26, 2024

If there is more than one gene for a given domain, retains the lowest e-value (case of full rRNA operon sequences).

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!
  • 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>).
  • 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).

@vaulot
Update summarize_barrnap.py
42a7556 
If there is more than one gene for a given domain,
retains the lowest e-value (case of full rRNA operon sequences).
@d4straub
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Thanks!
There are currently two failing tests (some are still running though). One test (test_multi) seems a github problem and I'll initiate a re-run later. However, linting complains about

bin/summarize_barrnap.py:
	31: Trailing whitespace

Could you rectify that?
Also it would be great is you could add a comment to the CHANGELOG.md in the 2.9.0dev section.

@vaulot
Update summarize_barrnap.py
76bbddd 
Remove extra space
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github-actions bot commented Mar 26, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3a3532d

+| ✅ 191 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-26 14:39:40

@d4straub
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Thanks again!

@d4straub d4straub merged commit 0926dc2 into nf-core:dev Mar 26, 2024
17 checks passed
@d4straub d4straub mentioned this pull request Mar 26, 2024
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@vaulot @d4straub