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Add Bakta meta mode #338

Merged
merged 5 commits into from
Feb 12, 2024
Merged

Add Bakta meta mode #338

merged 5 commits into from
Feb 12, 2024

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jasmezz
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@jasmezz jasmezz commented Feb 12, 2024

This adds the bakta --meta mode parameter (default: true).
Additionally, mention the defaults from nextflow.config in nextflow_schema.json for:

  • --annotation_bakta_db_downloadtype --> 'full'
  • --annotation_prokka_compliant --> true

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/funcscan 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,singularity --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 Feb 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b0317a2

+| ✅ 223 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 2.12.1
  • Run at 2024-02-12 15:39:29

@jasmezz jasmezz requested a review from a team February 12, 2024 14:51
jfy133
jfy133 approved these changes Feb 12, 2024
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@jasmezz @jfy133
Update CHANGELOG.md [skip ci]
9a83cf1 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@jasmezz jasmezz merged commit 11719fa into dev Feb 12, 2024
@jasmezz jasmezz deleted the bakta-meta-mode branch February 12, 2024 16:27
@jasmezz jasmezz mentioned this pull request Jul 29, 2024
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@jfy133 jfy133 jfy133 approved these changes

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@jasmezz @jfy133