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updating template #71

Merged
merged 5 commits into from
Feb 29, 2024
Merged

updating template #71

merged 5 commits into from
Feb 29, 2024

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jemten
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@jemten jemten commented Feb 28, 2024 •
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Lot's of changes with the new template. Also had to modify the pipeline code slightly to get it to work with these changes

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
  • 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).

@jemten jemten linked an issue Feb 28, 2024 that may be closed by this pull request
Update to v2.13 of nf-core TEMPLATE #70
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github-actions bot commented Feb 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d208fc6

+| ✅ 153 tests passed       |+
#| ❔ 317 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-29 10:17:07

@jemten jemten marked this pull request as ready for review February 28, 2024 16:05
@jemten jemten requested a review from Lucpen as a code owner February 28, 2024 16:05
Lucpen
Lucpen reviewed Feb 29, 2024
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bin/drop_filter_results.py Outdated Show resolved Hide resolved
@Lucpen Lucpen merged commit 922d548 into dev Feb 29, 2024
4 checks passed
@Lucpen Lucpen deleted the template-update branch February 29, 2024 10:46
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@Lucpen Lucpen Lucpen approved these changes

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Update to v2.13 of nf-core TEMPLATE
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@jemten @Lucpen