nf-core task.ext.args → Galaxy additional-options bag

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

Why a single bag, not per-flag inputs

nf-core modules expose task.ext.args (sometimes args2, args3) as the configuration escape hatch — pipelines override these per-process via modules.config. The bag is intentionally opaque: the module’s authors chose not to enumerate every flag of the upstream tool, so the wrapper inherits a one-string-of-CLI surface.

Galaxy has no per-step config layer; the natural mirror is one optional text <param> appended to the command line. Going further (per-flag inputs) re-enumerates the upstream tool’s CLI in Galaxy XML, which:

• Forces the wrapper author to track upstream releases at the flag level — the exact maintenance load nf-core declined.
• Doubles the cognitive surface for users: which flags are first-class, which need the bag.

The policy is: surface task.ext.args as a single bag. Promote individual flags to first-class <param>s only when the module already does (e.g., discard_trimmed_pass is a val input in fastp; that’s a <param type="boolean">, not part of the args bag).

Cited cases

Single-arg use → one extra_args text param

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

script:
def args = task.ext.args ?: ''
"""
samtools index -@ ${task.cpus} ${args} ${input}
"""

Galaxy:

<param argument="" name="extra_args" type="text" optional="true"
       label="Additional command-line options"
       help="Pass-through string appended to the upstream tool's CLI. Mirrors nf-core's task.ext.args escape hatch.">
  <sanitizer invalid_char="">
    <valid initial="string.printable">
      <remove value="&apos;"/>
    </valid>
  </sanitizer>
</param>

<command><![CDATA[
samtools index -@ \${GALAXY_SLOTS:-1} $extra_args '$input'
]]></command>

Args used to introspect → still one bag

modules/nf-core/fastp/main.nf reads its own task.ext.args to switch on --interleaved_in:

script:
def args = task.ext.args ?: ''
...
if ( task.ext.args?.contains('--interleaved_in') ) {
    """ ...fastp --stdout --in1 ... """
}

The convert Mold should not try to translate this introspection into Galaxy XML. Two reasonable options:

1. Surface extra_args and document in <help>: “Set --interleaved_in to enable interleaved-FASTQ mode.”
2. Promote the specific flag to a <param type="boolean"> (interleaved_in) and pass-through everything else via extra_args.

Option 2 is the IUC pattern (tools-iuc/tools/fastp/fastp.xml does exactly this for many flags); option 1 is the fast path the convert Mold defaults to. Record the choice in _provenance.yml.overrides so the reviewer can flag aggressive expansions for verification.

args2 / args3 → numbered bags

modules/nf-core/sratools/fasterqdump/main.nf:

def args  = task.ext.args  ?: ''
def args2 = task.ext.args2 ?: ''

Used to feed two distinct upstream invocations. Galaxy mapping: two text params (extra_args, extra_args2), each scoped to the relevant invocation in <command>. Document the mapping in <help>.

Sanitization

Galaxy’s default sanitizer rewrites quotes and backslashes — fine for a value like a sample name, fatal for a CLI fragment. Two options:

1. Permissive <sanitizer> block as shown above. Lets users include their own quoting; the convert Mold leans on <![CDATA[ ]]> in <command> for outer quoting.
2. sanitize="false" on the <param>. Simplest; trust that the user knows shell quoting. Acceptable for an opt-in advanced field.

The convert Mold defaults to (1) because it preserves the rest of Galaxy’s input safety machinery while opening the specific quote-removal behavior that breaks args bags.

Pitfalls

• Don’t double-quote the bag in <command>. '$extra_args' injects literal quotes around the entire string, breaking the user’s quoting.
• Watch for ${task.cpus} interpolation. nf-core scripts use ${task.cpus} for thread counts; Galaxy’s analog is \${GALAXY_SLOTS:-1}. Translate this directly; it does not belong in the args bag.
• Don’t surface task.ext.prefix. Modules use it for output filenames; Galaxy’s $input.element_identifier is the right substitute. See [[nfcore-meta-map-to-galaxy-params]].
• task.ext.when is the conditional gate for whether the process runs. It has no Galaxy analog (Galaxy’s tool runs unconditionally when invoked); ignore.

See also

• [[nfcore-meta-map-to-galaxy-params]] — sibling: handling identity vs behavior keys.
• [[convert-nfcore-module-to-galaxy-tool]] — Mold that consumes this pattern.
• tools-iuc/tools/fastp/fastp.xml — IUC’s per-flag promotion choice (option 2 above).