Add Zarr support to scanpy/pca

[ehsanestaji]

PR checklist

Part of #11559

This PR adds Zarr input/output support to scanpy/pca as a first scverse module slice.

Changes:

• Detect .zarr inputs and emit a matching .zarr AnnData output directory.
• Preserve existing .h5ad behavior for .h5ad inputs.
• Add zarr as an optional output channel and document it in meta.yml.
• Add a small AnnData Zarr fixture plus stub and real Zarr tests.
• Broadcast versions.yml on topic: versions.
• Avoid importing scanpy in the stub version command by using importlib.metadata.version("scanpy").

Validation run locally on 2026-05-19:

• conda run -n nfcore-topic nf-core modules lint scanpy/pca --local --plain-text

• conda run -n nfcore-topic prek run --files $(git diff --name-only)

• conda run -n nfcore-topic nf-test test modules/nf-core/scanpy/pca/tests/main.nf.test --profile docker --filter process --verbose

• conda run -n nfcore-topic nf-test test modules/nf-core/scanpy/pca/tests/main.nf.test --profile conda --filter process --verbose

• git diff --check

• 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.

• Broadcast software version numbers to topic: versions - See version_topics

• 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 scanpy/pca --profile docker
    • nf-core modules test scanpy/pca --profile singularity
    • nf-core modules test scanpy/pca --profile conda

[ehsanestaji]

Follow-up pushed in 774206f. This addresses the local/CI issues I could reproduce: versions.yml now broadcasts to topic: versions, the Zarr fixture metadata files have final newlines for pre-commit, and the h5ad test now checks output presence/content instead of MD5 snapshots that differ across runtimes.\n\nLocal validation passed on 2026-05-19:\n- conda run -n nfcore-topic nf-core modules lint scanpy/pca --local --plain-text\n- conda run -n nfcore-topic prek run --files $(git diff --name-only)\n- conda run -n nfcore-topic nf-test test modules/nf-core/scanpy/pca/tests/main.nf.test --profile docker --filter process --verbose\n- conda run -n nfcore-topic nf-test test modules/nf-core/scanpy/pca/tests/main.nf.test --profile conda --filter process --verbose\n- git diff --check\n\nThe GitHub workflow runs for this new commit currently show action_required before jobs start, so a maintainer may need to approve them when convenient.

[ehsanestaji]

Update: rebased this PR onto current nf-core/modules:master and marked it ready for review. Latest head is 71bbc5a11.\n\nFresh local validation after the rebase:\n- conda run -n nfcore-topic nf-core modules lint scanpy/pca --local --plain-text\n- conda run -n nfcore-topic prek run --files $(git diff --name-only upstream/master...HEAD)\n- conda run -n nfcore-topic nf-test test modules/nf-core/scanpy/pca/tests/main.nf.test --profile docker --filter process --verbose\n- git diff --check\n\nThe GitHub workflows are still awaiting maintainer approval before they can run.

[SPPearce]

You seem to have some files in the tests folder that aren't required.
Is there a zarr file that we could test on? But from the test-datasets.

[ehsanestaji]

Moved the Zarr fixture out of the module tests directory and updated the tests to use nf-core/test-datasets via params.modules_testdata_base_path. Since Zarr is directory-backed, the fixture is stored in test-datasets as a small .zarr.tar.gz archive and unpacked with UNTAR during nf-test setup.

Prerequisite test-data PR: nf-core/test-datasets#2076. I validated the module tests locally against that forked test-data branch; the official test-data URL will work once that PR is merged.

[SPPearce]

Can I suggest that you go to the #github-invitations in the nf-core slack, you can be added to the organisation so the tests run.

[ehsanestaji]

I requested access in the nf-core Slack #github-invitations channel. Once I’m added to the organisation, the CI should be able to run on this PR.

[nictru]

Please incorporate the feedback Lukas and I provided in #11756 so we can make sure the zarr support is structured the same way for all affected modules

[nictru]

Please follow the same structure as in #11756

[nictru]

Please keep the logic structure consistent with #11756