nf-core meta-map → Galaxy params

The nf-core meta map travels with the data channel as tuple val(meta), path(...). Galaxy has no metadata-channel equivalent — datasets carry only their own element_identifier, name, and format. The convert Mold’s job is to triage every meta key the script body reads.

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

Triage rule

Walk the module’s script: body for meta.<key> references. For each key, classify:

When in doubt, prefer dropping over surfacing. Galaxy users don’t expect to fill in metadata that the platform already tracks per-dataset.

Cited cases

Identity only → drop

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

process SAMTOOLS_INDEX {
    tag "${meta.id}"
    ...
    input:
    tuple val(meta), path(input)
    ...
    script:
    """
    samtools index -@ ${task.cpus} ${args} ${input}
    """
}

meta.id appears only in the tag directive (Nextflow log line) — never in the script. Drop entirely; Galaxy’s history-item identity is the dataset’s element_identifier. The convert Mold’s <command> does not need to reference meta.id at all.

Behavior-driving (boolean) → <conditional>

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

script:
def args = task.ext.args ?: ''
...
if ( task.ext.args?.contains('--interleaved_in') ) {
    """ ...fastp --stdout --in1 ... """          // interleaved (single-input shape)
} else if (meta.single_end) {
    """ ...fastp --in1 ... """                   // single-end
} else {
    """ ...fastp --in1 ... --in2 ... """         // paired
}

meta.single_end gates a hard branch — the command line is materially different. The first branch (interleaved) is task.ext.args-driven, not meta-driven, and collapses into the single-input shape (see [[nfcore-task-ext-args-to-galaxy-additional-options]]). Galaxy mapping for the meta gate: a <conditional name="single_paired"> whose selector drives both the <inputs> shape (per [[nfcore-channel-input-to-galaxy-collection]] — two arms single + paired_collection) and the <command> branching:

<command><![CDATA[
fastp
#if $single_paired.single_paired_selector == "single"
    --in1 '$single_paired.in1'
#else
    --in1 '$single_paired.in1' --in2 '$single_paired.in2'
#end if
]]></command>

Same key, two collaborating mappings: input shape and command shape. The convert Mold should treat the <conditional> as a single unit gated by the meta key, not two independent translations.

Behavior-driving (multi-arm) → <param type="select">

modules/nf-core/cat/fastq/main.nf reads meta.single_end to switch between cat-one-stream and cat-two-streams. Same shape as fastp; <conditional> over the same selector.

Pass-through tag → optional text param

When a module writes meta.id into a non-output-name place (e.g., a header field of a derived file), the convert Mold can either:

1. Default to $input.element_identifier in <command> and not surface the param. (Preferred — Galaxy users already named the dataset.)
2. Surface as <param name="sample_id" type="text" optional="true" label="Sample ID (defaults to dataset name)">, defaulting to $input.element_identifier.

Option 1 is right unless the upstream tool genuinely supports two distinct identifiers for one input (rare).

Pitfalls

• Don’t surface meta.id as a required user input. This is the most common over-translation. Galaxy already has identifier semantics; doubling them up confuses users and breaks collection-aware idioms.
• Don’t expand a meta-map’s full key set. Pipelines extend the meta map with arbitrary keys (meta.run, meta.lane, meta.barcode); only the keys the module’s own script body reads matter at conversion time.
• Behavior-driving keys must surface. Hiding meta.single_end inside the wrapper (e.g., always emitting the paired branch) silently breaks single-end runs. The conditional is non-negotiable when the script branches on it.
• meta.strandedness is rare in modules; it usually surfaces as a separate val input. Don’t auto-emit a strandedness <param> based on key name; check the script body actually reads it.

See also

• [[nfcore-channel-input-to-galaxy-collection]] — sibling pattern: meta-driven input shape decisions.
• [[convert-nfcore-module-to-galaxy-tool]] — Mold that consumes this pattern.