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Merged
khersameesh24 merged 2 commits into from
Oct 25, 2025
Merged

Codespace scaling giggle 4vrjwqp5rv4375jr #10

khersameesh24 merged 2 commits into from
Oct 25, 2025

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@khersameesh24 khersameesh24 commented Oct 25, 2025

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/spatialxe 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).

@khersameesh24 khersameesh24 merged commit 86b47fa into dev Oct 25, 2025
2 of 4 checks passed
@khersameesh24 khersameesh24 deleted the codespace-scaling-giggle-4vrjwqp5rv4375jr branch October 25, 2025 21:25
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github-actions bot commented Oct 25, 2025

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 547d9f1

+| ✅ 245 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  11 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialxe_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialxe_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialxe_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-10-25 21:26:47

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@khersameesh24