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Improve bracken tagging #330

Merged
merged 4 commits into from
Jul 19, 2023
Merged

Improve bracken tagging #330

merged 4 commits into from
Jul 19, 2023

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jfy133
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@jfy133 jfy133 commented Jul 19, 2023 •
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closes #329

image

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).

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/taxprofiler master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/taxprofiler dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@jfy133 jfy133 changed the base branch from master to dev July 19, 2023 06:56
jfy133
jfy133 commented Jul 19, 2023
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jfy133
jfy133 commented Jul 19, 2023
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@jfy133 jfy133 requested a review from a team July 19, 2023 06:56
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github-actions bot commented Jul 19, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 476f87f

+| ✅ 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 07:20:51

@LilyAnderssonLee
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Great job on making the Kraken and Bracken processes more recognizable in the log file!!!

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jfy133 commented Jul 19, 2023

@LilyAnderssonLee if you're happy with it, please press the green 'review' and press' approve :)

@jfy133 jfy133 merged commit 72dbc0f into dev Jul 19, 2023
20 checks passed
@jfy133 jfy133 deleted the improve-brack-tagging branch July 19, 2023 08:43
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

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Rename process name of kraken2 that goes to bracken
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@jfy133 @LilyAnderssonLee