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Add custom script licences to all tools#581

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jfy133 merged 3 commits intodevfrom
custom-script-licence
Feb 12, 2024
Merged

Add custom script licences to all tools#581
jfy133 merged 3 commits intodevfrom
custom-script-licence

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@jfy133 jfy133 commented Feb 9, 2024

Closes #570

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).

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github-actions Bot commented Feb 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7359174

+| ✅ 211 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • 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 2024-02-09 13:30:41

HadrienG
HadrienG approved these changes Feb 9, 2024
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lgtm

@jfy133 jfy133 merged commit 9a67aad into dev Feb 12, 2024
@jfy133 jfy133 deleted the custom-script-licence branch February 12, 2024 16:17
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@HadrienG HadrienG HadrienG approved these changes

@skrakau skrakau Awaiting requested review from skrakau

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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@jfy133 @HadrienG