UNZIP: modernize to latest nf-core conventions

[maxcumminsandfred-lab]

Summary

Migrate the unzip module from legacy cat <<-END_VERSIONS > versions.yml heredoc to the modern eval() inline output with topic: versions. Remove versions.yml heredoc from stub block (eval runs automatically in stub mode). Update dependent subworkflows to handle the removal of .out.versions.

Changes

• modules/nf-core/unzip/main.nf: Replace heredoc version output with eval('7za --help | sed -n "s/.*p7zip Version //p" | sed "s/ .*//"') and topic: versions. Remove heredoc from both script and stub blocks.
• modules/nf-core/unzip/meta.yml: Add topics: and versions_7za: output sections (auto-generated by lint --fix). Remove stale versions: versions.yml output entry.
• modules/nf-core/unzip/tests/main.nf.test.snap: Updated snapshots reflecting new version tuple format ["UNZIP", "7za", "16.02"].
• subworkflows/nf-core/archive_extract/main.nf: Remove versions variable and emit entirely — all 3 included modules (GUNZIP, UNTAR, UNZIP) now use topic: versions, so subworkflow-level version collection is no longer needed.
• subworkflows/nf-core/archive_extract/meta.yml: Remove versions output entry.
• subworkflows/nf-core/archive_extract/tests/main.nf.test.snap: Updated snapshot (no longer includes versions key).
• subworkflows/nf-core/homer_groseq/main.nf: Remove ch_versions.mix(UNZIP.out.versions) — UNZIP now emits via topic. HOMER modules remain legacy and still use ch_versions.

Verification

• Lint: PASSED (46 passed, 0 warnings, 0 failed)
• Module tests: 2 passed, 0 failed (docker profile)
• archive_extract tests: 1 passed, 0 failed (docker profile)
• homer_groseq tests: 4 passed, 0 failed (docker profile)
• Snapshots: stable (verified across 2 runs for all test suites)

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 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 <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

Co-Authored-By: Claude Opus 4.6 (1M context) noreply@anthropic.com

[maxcumminsandfred-lab]

Should archive_extract retain a versions emit after all modules migrate to topic: versions?

GUNZIP and UNTAR appear to already be migrated, so with this UNZIP PR all 3 modules use topics. I removed ch_versions.mix() and the versions emit since topic outputs appear to bypass workflow.out at the subworkflow level.

Checking for precedent: I found 69 multi-module subworkflows where all included modules appear to use topic: versions. 63 have no ch_versions or versions emit. The remaining 6 still emit versions but the channel appears empty. I was unable to find any
subworkflow snapshot containing modern-style version tuples.

Examples that appear to follow this pattern:

bam_rseqc (8 modules): https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/bam_rseqc

fasta_index_bismark_bwameth (5 modules):
https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/fasta_index_bismark_bwameth

Is this correct, or should fully-migrated subworkflows retain versions in some form?