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Merged
camlloyd merged 23 commits into from
Jan 22, 2026
Merged

update module: spaceranger #8911

camlloyd merged 23 commits into from
Jan 22, 2026
+113 −65

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@camlloyd camlloyd commented Aug 15, 2025 •
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PR checklist

Closes #8910 by bumping the spaceranger version in the Dockerfile, also update the README.

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@camlloyd camlloyd marked this pull request as ready for review August 15, 2025 21:45
edmundmiller
edmundmiller approved these changes Aug 23, 2025
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Awesome! Looks good to me, thanks!

camlloyd
camlloyd commented Aug 25, 2025
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edmundmiller and others added 2 commits August 26, 2025 09:43
@edmundmiller @claude
feat: add fork PR warning for container changes in wave workflow
7cce577 
Add a new job that warns when fork PRs modify Dockerfile or environment.yml files.
This addresses the issue where container builds silently fail to run on fork PRs
due to security restrictions, providing clear feedback to contributors and maintainers.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
@edmundmiller
build: Rebuild and push to quay.io
cff1bb7
@edmundmiller edmundmiller requested review from a team as code owners August 26, 2025 15:39
@nathanweeks
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nathanweeks commented Oct 10, 2025

Is there anything left to be done for this PR? I'd like to see Space Ranger 4.0.1 available for use by nf-core/spatialvi to fix an issue I have running that pipeline.

FloWuenne
FloWuenne approved these changes Oct 14, 2025
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edmundmiller
edmundmiller approved these changes Oct 14, 2025
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LGTM!

@camlloyd @FloWuenne
Update modules/nf-core/spaceranger/count/tests/nextflow.config
34b516a 
Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
@camlloyd camlloyd enabled auto-merge October 14, 2025 19:44
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FloWuenne commented Oct 15, 2025

@edmundmiller Any issues with the remaining failing tests? Are the lint failures valid? I can't quite make out why the nf-tests are failing.

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nathanweeks commented Nov 6, 2025

There seems to be a unicode character (?) in the quay.io URLs that's causing nf-core module lint spaceranger to fail with three container_links: Unable to connect to container URL errors.

e.g., in vim, I see the following for nf-core/modules/spaceranger/*/main.nf:

    container "quay<200b>.io/nf-core/spaceranger:9c5e7dc93c32448e"

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nathanweeks commented Nov 6, 2025

There seems to be a unicode character (?) in the quay.io URLs that's causing nf-core module lint spaceranger to fail with three container_links: Unable to connect to container URL errors.

e.g., in vim, I see the following for nf-core/modules/spaceranger/*/main.nf:

    container "quay<200b>.io/nf-core/spaceranger:9c5e7dc93c32448e"

After removing the "insisible" character (apparently a zero-width space), nf-core module lint spaceranger returns three errors with message:

container_links: quay.io/nf-core/spaceranger:9c5e7dc93c32448e container name found, please use just 'organisation/container:tag' instead.

Using the following image format resolves those lint errors:

    container "nf-core/spaceranger:9c5e7dc93c32448e"

@camlloyd camlloyd disabled auto-merge January 22, 2026 13:10
@camlloyd camlloyd added this pull request to the merge queue Jan 22, 2026
Merged via the queue into nf-core:master with commit a92090d Jan 22, 2026
39 of 40 checks passed
@camlloyd camlloyd deleted the spaceranger branch January 22, 2026 14:59
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@edmundmiller edmundmiller edmundmiller approved these changes

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update module: spaceranger

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