modules bump-versions: match nf-core container formatting in main.nf

[asharaali]

nf-core modules bump-versions rewrites the container directive in main.nf after the Wave build, and the block it writes puts the ternary operators at column 0 and pads the inside of ${...}:

    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e6/e613097.../data'
:         'community.wave.seqera.io/library/fgumi:0.6.0--c97194d17da0d1cd' }"

That is the shape nf-core/modules#12756 had to undo by hand across every bumped module.

Everywhere else in nf-core/modules, and in the modules this repo ships in nf_core/pipeline-template/modules/nf-core/{fastqc,multiqc}/main.nf, the directive reads:

    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e6/e613097.../data'
        : 'community.wave.seqera.io/library/fgumi:0.6.0--c97194d17da0d1cd'}"

update_main_nf_container() in nf_core/modules/containers.py builds the replacement from an f-string that emits ? {inner_indent} where it means {inner_indent}? . Moving the operators behind the indent and dropping the padding inside ${...} is the whole change.

Verification

tests/modules/test_containers.py does not run on my machine: TestModules.setUp builds a pipeline through nextflow config, and nextflow is not installed here. On unmodified dev all 38 tests in that file error out in setup, so a local pass/fail there would mean nothing either way — the new test is written for CI.

What I could check directly, by driving ModuleContainers.update_main_nf_container() against a temporary modules repo:

• on dev, the rewritten directive is byte-identical to the broken block above
• with this patch, it is byte-identical to modules/nf-core/samtools/sort/main.nf on nf-core/modules master

ruff check and ruff format --check are clean on both changed files.

CHANGELOG

Not touched. CHANGELOG.md has no running dev section since 4.1.0 shipped, and .github/workflows/changelog.py appends into one that already exists — happy for @nf-core-bot changelog to add the entry once there is a section to add it to, or to add it myself if you would rather pick the version heading now.

Fixes #4452

[mashehu]

please join the nf-core org via slack to get the CI running.

[mashehu]

@nf-core-bot changelog

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.39%. Comparing base (fc17087) to head (40fb108).

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