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PR2 exact species assignment now without taxa ending with sp. #599

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merged 2 commits into from
Jun 26, 2023
Merged

PR2 exact species assignment now without taxa ending with sp. #599

merged 2 commits into from
Jun 26, 2023

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d4straub
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@d4straub d4straub commented Jun 23, 2023 •
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Closes #593.

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.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jun 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 808185b

+| ✅ 154 tests passed       |+
#| ❔   3 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 2.8
  • Run at 2023-06-26 07:39:36

@d4straub d4straub mentioned this pull request Jun 23, 2023
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jtangrot
jtangrot approved these changes Jun 26, 2023
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LGTM!

bin/taxref_reformat_pr2.sh
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I suggest to add a comment on the last part too, i.e. the awk part that removes " sp".

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Thanks, yes, will do!

@d4straub d4straub merged commit 3115488 into nf-core:dev Jun 26, 2023
@d4straub d4straub deleted the pr2-species-assignment branch June 26, 2023 12:21
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@jtangrot jtangrot jtangrot approved these changes

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@d4straub @jtangrot