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Update taxpasta #355

Merged
merged 5 commits into from
Aug 26, 2023
Merged

Update taxpasta #355

merged 5 commits into from
Aug 26, 2023

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sofstam
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@sofstam sofstam commented Aug 25, 2023

This PR updates taxpasta module to 0.5.0

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/taxprofiler 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).

@sofstam sofstam requested a review from a team August 25, 2023 14:29
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github-actions bot commented Aug 25, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b85d397

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-26 06:57:33

jfy133
jfy133 requested changes Aug 25, 2023
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  • Need changelog depedency table update
  • Need to add support for the new flags (rank lineage, for example)

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sofstam commented Aug 25, 2023

We already have support for:

    taxpasta_add_name                       = false
    taxpasta_add_rank                       = false
    taxpasta_add_lineage                    = false
    taxpasta_add_idlineage                  = false

Or do you mean something different?

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jfy133 commented Aug 25, 2023

Sorry new flag (singular)

https://taxpasta.readthedocs.io/en/latest/quick_reference/standardise/

--add-rank-lineage as added in taxprofiler/taxpasta#130

jfy133
jfy133 approved these changes Aug 26, 2023
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jfy133
jfy133 reviewed Aug 26, 2023
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@jfy133 jfy133 merged commit 06c6f14 into nf-core:dev Aug 26, 2023
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@sofstam @jfy133