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Nf core template update #461

Merged
merged 8 commits into from Dec 21, 2023
Merged

Nf core template update #461

merged 8 commits into from Dec 21, 2023

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jemten
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@jemten jemten commented Dec 20, 2023 •
edited

nf-core 2.11.1 template update

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 Dec 20, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 41e63b3

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2023-12-20 16:24:31

@jemten jemten marked this pull request as ready for review December 20, 2023 16:36
@jemten jemten requested a review from Lucpen December 20, 2023 16:41
Lucpen
Lucpen approved these changes Dec 21, 2023
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@Lucpen Lucpen left a comment

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Great! Let 's see if this fixes test for other PRs :D

@jemten jemten merged commit e3160e5 into nf-core:dev Dec 21, 2023
8 checks passed
@jemten jemten deleted the nf-core-tools_update branch December 21, 2023 08:33
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@Lucpen Lucpen Lucpen approved these changes

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@jemten @Lucpen @nf-core-bot