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Disambiguate same-db name but bracken step kraken from profile mergin… #406

Merged
merged 5 commits into from
Oct 26, 2023
Merged

Disambiguate same-db name but bracken step kraken from profile mergin… #406

merged 5 commits into from
Oct 26, 2023

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jfy133
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@jfy133 jfy133 commented Oct 22, 2023

closes #395

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).

@jfy133 jfy133 marked this pull request as draft October 22, 2023 04:25
@jfy133 jfy133 added the WIP Work in progress label Oct 22, 2023
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github-actions bot commented Oct 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit da8bf5a

+| ✅ 159 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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 2.10
  • Run at 2023-10-25 13:11:07

@jfy133 jfy133 marked this pull request as ready for review October 23, 2023 12:03
@jfy133 jfy133 removed the WIP Work in progress label Oct 23, 2023
@jfy133 jfy133 requested a review from a team October 23, 2023 12:03
@sofstam sofstam self-requested a review October 24, 2023 08:38
Midnighter
Midnighter approved these changes Oct 25, 2023
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Code looks fine to me!

subworkflows/local/profiling.nf Outdated Show resolved Hide resolved
subworkflows/local/standardisation_profiles.nf Outdated Show resolved Hide resolved
subworkflows/local/standardisation_profiles.nf Outdated Show resolved Hide resolved
subworkflows/local/visualization_krona.nf Outdated Show resolved Hide resolved
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da8bf5a 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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jfy133 commented Oct 26, 2023

Tested and confirm same behaviour with simplified strucutre 👍

@jfy133 jfy133 merged commit 267e1a1 into dev Oct 26, 2023
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@jfy133 jfy133 deleted the krona-ktimporttext-input-collision-fix branch October 26, 2023 03:39
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@Midnighter Midnighter Midnighter approved these changes

@sofstam sofstam Awaiting requested review from sofstam

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