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add Prokka to MultiQC #295

Merged
merged 6 commits into from
Jul 19, 2023
Merged

add Prokka to MultiQC #295

merged 6 commits into from
Jul 19, 2023

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louperelo
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@louperelo louperelo commented Jul 13, 2023 •
edited by jfy133
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partly Closes issue #277

The Prokka module was added to the MultiQC output. For the other annotation tools (Prodigal, Pyrodigal, Bakta) there are no MultiQC modules yet.

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,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).

@louperelo louperelo requested review from jfy133 and jasmezz July 13, 2023 13:25
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github-actions bot commented Jul 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 74b59d0

+| ✅ 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 2023-07-19 09:12:55

@louperelo
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@nf-core-bot fix linting

@louperelo
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@nf-core-bot fix linting

jfy133
jfy133 approved these changes Jul 19, 2023
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Fine for now, other annotation modules can come later

workflows/funcscan.nf Outdated Show resolved Hide resolved
@louperelo @jfy133
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74b59d0 
Co-authored-by: James A. Fellows Yates <[email protected]>
@louperelo louperelo merged commit c61ea09 into nf-core:dev Jul 19, 2023
21 of 24 checks passed
@louperelo louperelo deleted the prokka_mqc branch July 19, 2023 09:40
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@jfy133 jfy133 jfy133 approved these changes

@jasmezz jasmezz Awaiting requested review from jasmezz

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@louperelo @jfy133 @nf-core-bot