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Update github action to the dev one in nf-core tools #137

Merged
merged 5 commits into from
May 27, 2024
Merged

Update github action to the dev one in nf-core tools #137

merged 5 commits into from
May 27, 2024

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LaurenceKuhl
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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/crisprseq 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).

@github-actions GitHub Actions
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github-actions bot commented May 6, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 44913f4

+| ✅ 218 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.2.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-24 07:06:04

@LaurenceKuhl
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hey @mirpedrol the linting is failing because we modified some files, should i add them in the lint ignore? Or should we look at the template update PR anyway?

@LaurenceKuhl LaurenceKuhl merged commit 29a035d into nf-core:dev May 27, 2024
11 of 12 checks passed
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@LaurenceKuhl