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Template update nf-core tools 2.9 #87

Merged
merged 1 commit into from
Jul 19, 2023
Merged

Template update nf-core tools 2.9 #87

merged 1 commit into from
Jul 19, 2023

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tillenglert
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I merged the template update on my fork, as it was based on a previous dev version with a missing PR, and some major merge conflict needed to be solved.
As soon as this PR is merged, we can close the other one.

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/metapep 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).

@tillenglert tillenglert requested a review from skrakau July 13, 2023 11:18
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github-actions bot commented Jul 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1b605b1

+| ✅ 155 tests passed       |+
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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 full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • 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
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-13 11:19:56

skrakau
skrakau approved these changes Jul 19, 2023
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LGTM!

@tillenglert tillenglert merged commit 8913959 into nf-core:dev Jul 19, 2023
10 checks passed
@tillenglert tillenglert deleted the Template_update_2.9 branch July 19, 2023 08:32
@tillenglert tillenglert mentioned this pull request Jul 19, 2023
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@skrakau skrakau skrakau approved these changes

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@tillenglert @skrakau