Add stub block and migrate emmtyper to topic channels

[HReed1]

Description

Migrates the emmtyper module to use topic channels for version outputs and adds a stub block, addressing both #4570 and #11389.

This is a pilot PR to validate the combined stubs + topics migration pattern before batch-submitting the remaining ~39 modules.

Changes

main.nf

• Replaced path "versions.yml", emit: versions with single-quoted eval() topic output:

  tuple val("${task.process}"), val('emmtyper'), eval('emmtyper --version 2>&1 | sed "s/^.*emmtyper v//"'), topic: versions, emit: versions_emmtyper
  

• Removed the cat <<-END_VERSIONS HEREDOC block from the script
• Added stub: block with touch ${prefix}.tsv

meta.yml (auto-fixed via nf-core modules lint --fix)

• Replaced versions: output (versions.yml file) with versions_emmtyper: tuple definition
• Added topics: block below outputs

tests/main.nf.test

• Added stub test: test("test-emmtyper - stub") with options "-stub"
• Uses sanitizeOutput(process.out) per nft-utils convention

Validation

• nf-core modules lint emmtyper → 51/51 passed, 0 warnings, 0 failures
• nf-core modules test emmtyper --update --profile docker → All tests passed, snapshots stable
• eval() uses single-quoted string with direct pipe (canonical pattern from shapeit5)

PR checklist

Closes #4570 (partial — emmtyper only)
Related to #10832

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• 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 emmtyper --profile docker
    • nf-core modules test emmtyper --profile singularity
    • nf-core modules test emmtyper --profile conda

[heuermh]

I'm not sure why conda tests are failing when docker and singularity look fine, the error appears to be in the version check

    > ERROR ~ Error executing process > 'EMMTYPER (test)'
    > 
    > Caused by:
    >   Unable to evaluate output
    > 
    > 
    > Command executed:
    > 
    >   echo $(emmtyper --version 2>&1) | sed 's/^.*emmtyper v//'
    > 
    > Command exit status:
    >   2
    > 
    > Command output:
    >   bash: -c: line 2: syntax error near unexpected token `('
    >   bash: -c: line 2: `  parser = self.make_parser(ctx)'

[HReed1]

Thanks for flagging this @heuermh! The issue was the eval() quoting — the echo $() wrapper was capturing Python traceback output containing parentheses, which bash was interpreting as syntax.

Fixed in the latest push: switched to single-quoted eval('emmtyper --version 2>&1 | sed "s/^.*emmtyper v//"') with a direct pipe (matching the canonical pattern from shapeit5). Also added sanitizeOutput() to the test snapshots per @famosab's feedback on #11349.

[HReed1]

Thank you @SPPearce for all the feedback. We are current Green on all Github Actions for this PR.