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Replace erikfas/spatialvi with Seqera image #127

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Merged
cavenel merged 6 commits into from
Nov 5, 2025
Merged

Replace erikfas/spatialvi with Seqera image #127

cavenel merged 6 commits into from
Nov 5, 2025

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@fasterius fasterius commented Oct 30, 2025

Replace the old erikfas/spatialvi Docker image with one created with Seqera containers instead. The old image was at one point required, partly due to issues with Quarto and Conda, partly due to problems with the required Python environment in general.

The old image also used a multi-stage build for Quarto, but the new Seqera image install Quarto using Conda instead, which now works.

This update does not change any versions of the environment itself, opting to stay with the exact versions of the old environment, even though more up to date packages are available. The newer versions should also be tested at some point.

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/spatialvi branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

@fasterius
Replace erikfas/spatialvi with Seqera image
d0c9bef 
Replace the old `erikfas/spatialvi` Docker image with one created with
Seqera containers instead. The old image was at one point required,
partly due to issues with Quarto and Conda, partly due to problems with
the required Python environment in general.

The old image also used a multi-stage build for Quarto, but the new
Seqera image install Quarto using Conda instead, which now works.

This update does not change any versions of the environment itself,
opting to stay with the exact versions of the old environment, even
though more up to date packages are available. The newer versions should
also be tested at some point.
@fasterius fasterius self-assigned this Oct 30, 2025
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github-actions bot commented Oct 30, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 565782d

+| ✅ 214 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 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 3.4.1
  • Run at 2025-11-04 15:30:24

@fasterius fasterius requested a review from cavenel November 5, 2025 08:17
@cavenel cavenel merged commit 8552968 into dev Nov 5, 2025
14 checks passed
@cavenel cavenel mentioned this pull request Nov 7, 2025
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