nf-core versions emit → Galaxy <version_command>

Cited modules pinned to nf-core/modules@9b261a459473bc8e2d830bfc626f480c0733f4fe.

Every nf-core module emits a tool-version string. Galaxy’s <version_command> is the natural sink. Two emission shapes are both common in current nf-core/modules:

1. topic: versions (Nextflow 24+) — modern; an output tuple with eval(...) capturing the version string.
2. cat <<-END_VERSIONS > versions.yml heredoc — older; still present in many modules.

The convert Mold’s job is the same either way: extract the primary tool’s version-line command, strip Nextflow escaping, drop the versions channel from outputs, and emit <version_command>.

Cited cases

topic: versions style → strip eval('...'), keep the inner command

modules/nf-core/fastp/main.nf:

output:
...
tuple val("${task.process}"), val('fastp'),
      eval('fastp --version 2>&1 | sed -e "s/fastp //g"'),
      emit: versions_fastp, topic: versions

Galaxy:

<version_command><![CDATA[fastp --version 2>&1 | sed -e 's/fastp //g']]></version_command>

Mechanical translation: take the eval(...) argument verbatim, strip nothing (no escaping needed for eval(...) content), wrap in <![CDATA[ ]]>. Done.

modules/nf-core/samtools/sort/main.nf:

tuple val("${task.process}"), val('samtools'),
      eval("samtools version | sed '1!d;s/.* //'"),
      topic: versions, emit: versions_samtools

→

<version_command><![CDATA[samtools version | sed '1!d;s/.* //']]></version_command>

Heredoc style → strip \$(...) escaping

modules/nf-core/shasta/main.nf:

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    shasta: \$(shasta --version | head -n 1 | cut -f 3 -d " ")
END_VERSIONS

The \$( ... ) is Nextflow escaping for “let bash run this when the script runs, don’t expand at Nextflow parse time.” Galaxy’s <version_command> is invoked directly by Galaxy at tool-introspection time — no Nextflow layer, no escaping needed. Strip the leading backslash:

<version_command><![CDATA[shasta --version | head -n 1 | cut -f 3 -d " "]]></version_command>

Mapping rules

• Single-tool module → one <version_command>. Pick the one tool the module wraps (the tool whose name matches meta.yml.tools[0] or the module’s own slug).
• Multi-tool module (mulled) → still one <version_command> for the primary tool. Galaxy’s <version_command> is single-string. Document the other tools’ versions in <help> text; they’re surfaced by BioContainers metadata at runtime, not by the wrapper.
• Drop the versions output channel. It has no Galaxy analog — Galaxy’s <requirements> + <version_command> carry the same information end-to-end. The convert Mold should never emit a Galaxy <data> for the versions channel.

Multiqc-style edge cases

modules/nf-core/multiqc/main.nf deliberately emits its versions outside the topic: versions channel:

// MultiQC should not push its versions to the `versions` topic.
// Its input depends on the versions topic to be resolved
// thus outputting to the topic will let the pipeline hang forever
tuple val("${task.process}"), val('multiqc'),
      eval('multiqc --version | sed "s/.* //g"'), emit: versions

Translation is identical: extract the eval(...) argument; emit one <version_command>. The pipeline-level rationale (avoiding a topic-channel deadlock) doesn’t carry into Galaxy — there’s no topic mechanism here.

Pitfalls

• Don’t escape backslashes twice. \$(...) in Nextflow becomes $(...) in the bash that Nextflow runs. Galaxy runs the <version_command> directly via subprocess — $(...) works as-is.
• Sed expressions need single-quoting. Inside <![CDATA[ ]]>, single quotes survive intact; double-quoted seds need careful escaping if they include $. Default to <![CDATA[...]]> + single-quoted sed.
• Tools that print version to stdout vs stderr. Use the same redirection as the upstream module (2>&1 if the module uses it). Don’t optimize away — the inversion can mask the actual version string.
• Tools without a --version flag. Some modules use <tool> -h | head -n 1 | awk '...'. Preserve the exact pipeline; Galaxy’s <version_command> is bash, not nextflow-eval.

See also

• [[convert-nfcore-module-to-galaxy-tool]] — Mold that consumes this pattern.
• tools-iuc/tools/fastp/fastp.xml — IUC’s <version_command> posture (often shorter than nf-core’s because IUC wraps a single tool).