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Patch release PR: 2.5.4 #585

Merged
merged 16 commits into from
Feb 12, 2024
Merged

Patch release PR: 2.5.4 #585

merged 16 commits into from
Feb 12, 2024

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jfy133
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@jfy133 jfy133 commented Feb 12, 2024

  • Adds licenses to all script files
  • Fixes the directory-input input channel for GTDB (module requires list of contents, rather than just the dir itself)
  • Turns off quality filtering during GTDB in test profiles (When running manually, as can't run on GHA as database is too big)

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/mag 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

CarsonJM
CarsonJM approved these changes Feb 12, 2024
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@jfy133 @CarsonJM
Update conf/test.config
07ada2a 
Co-authored-by: Carson J Miller <[email protected]>
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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 07ada2a

+| ✅ 210 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.4
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • 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
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-12 16:45:45

@jfy133 jfy133 merged commit e486bb2 into master Feb 12, 2024
27 of 28 checks passed
@jfy133 jfy133 mentioned this pull request Feb 12, 2024
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@maxulysse maxulysse maxulysse approved these changes

@CarsonJM CarsonJM CarsonJM approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

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@jfy133 @maxulysse @CarsonJM