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Merged
fasterius merged 8 commits into from
Jul 4, 2025
Merged

Futureproofing #115

fasterius merged 8 commits into from
Jul 4, 2025

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@fasterius fasterius commented Jun 18, 2025

This PR makes changes according to the new Nextflow strict syntax, as well as some minor formatting and harmonisation changes.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

@fasterius fasterius requested a review from cavenel June 18, 2025 10:59
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github-actions bot commented Jun 18, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5422297

+| ✅ 215 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-18 11:01:59

@fasterius fasterius marked this pull request as ready for review June 18, 2025 11:13
@fasterius fasterius merged commit a61954f into dev Jul 4, 2025
12 checks passed
@fasterius fasterius deleted the futureproofing branch July 4, 2025 15:38
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@cavenel cavenel cavenel approved these changes

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