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Merged
Felix-Kummer merged 6 commits into from
Dec 16, 2024
Merged

Adressing more reviewer comments for 1.0.0 #12

Felix-Kummer merged 6 commits into from
Dec 16, 2024

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@Felix-Kummer
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@Felix-Kummer Felix-Kummer commented Dec 16, 2024

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/rangeland 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).

@Felix-Kummer Felix-Kummer requested a review from jfy133 December 16, 2024 14:02
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nf-core-bot commented Dec 16, 2024

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 16, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e0377eb

+| ✅ 202 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this 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 ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-16 14:05:08

@Felix-Kummer Felix-Kummer merged commit e90a0d1 into nf-core:dev Dec 16, 2024
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@jfy133 jfy133 jfy133 approved these changes

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@Felix-Kummer @nf-core-bot @jfy133