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Changes to tackle revision for hotfix 1.0.1 - #202

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heylf merged 4 commits into
nf-core:devfrom
heylf:1.0.1
Aug 4, 2026
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Changes to tackle revision for hotfix 1.0.1#202
heylf merged 4 commits into
nf-core:devfrom
heylf:1.0.1

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@heylf

@heylf heylf commented Aug 4, 2026 •
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Why?

Incorperating revision of #193 from @erikrikarddaniel

Summary

  • adding new conf/tests folder and adding new test to check the bugfixes
  • Adds a real end-to-end test for the coordinate mode pipeline (not just the existing stub test), and updates the .nftignore list so the new test's snapshot comparison ignores known non-deterministic outputs.
  • Whitespace-only alignment fix. In each affected subworkflows/local/**/main.nf, the include { XENIUMRANGER_IMPORTSEGMENTATION } statement gains one extra space before the closing brace so its column lines up with the neighboring include statements in the same block. No logic 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!
  • 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.

@github-actions

github-actions Bot commented Aug 4, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Aug 4, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b1b0969

+| ✅ 286 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 1.0.1
  • 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.
  • schema_lint - Schema 'description' should be 'A pipeline for spatialomics 10x Xenium In Situ data.'
    Found: 'A pipeline to process spatialomics data from 10x Xenium In Situ or 10x Atera.'

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/linting_comment.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-spatialaxe_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialaxe_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialaxe_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-04 12:54:13

@heylf heylf changed the title 1.0.1 Changes to tackle revision for hotfix 1.0.1 Aug 4, 2026
@heylf heylf mentioned this pull request Aug 4, 2026
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erikrikarddaniel
erikrikarddaniel approved these changes Aug 4, 2026
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@erikrikarddaniel erikrikarddaniel left a comment

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👍

@heylf
heylf merged commit 104575f into nf-core:dev Aug 4, 2026
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@heylf @erikrikarddaniel