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Add MultiQC support for Space Ranger #70

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Add MultiQC support for Space Ranger #70

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fasterius
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@fasterius fasterius commented Mar 1, 2024 •
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This PR adds MultiQC support for Space Ranger, which was introduced in MultiQC 1.21.

This partially solves #40, but not downstream analyses.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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>).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.

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github-actions bot commented Mar 1, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit f8c2863

+| ✅ 161 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowSpatialtranscriptomics.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline 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

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialtranscriptomics_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialtranscriptomics_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialtranscriptomics_logo_dark.png
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-01 10:20:54

@fasterius
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Testing fails because of the SpatialDE Python module, which will be removed once #67 is finished, so leaving this PR as-is for now.

@fasterius fasterius self-assigned this Mar 4, 2024
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Closing this PR in favour of the consolidated #67.

@fasterius fasterius closed this Mar 7, 2024
@fasterius fasterius deleted the multiqc-spaceranger branch April 18, 2024 11:15
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