update module: spaceranger

[camlloyd]

PR checklist

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

• [x] 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:
    • [x] 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

[nathanweeks]

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]

@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.

[nathanweeks]

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"

[nathanweeks]

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"