Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Inherit open entries rather than re-deriving them, close the ones this brief's input, output, and label decisions settle, and append interface obligations the pipeline leaves open — a params entry with no Galaxy input, an emitted-but-unpublished output, a channel shape no collection maps cleanly onto.

Verify

Promote after a worked run shows entries this Mold appends or resolves are consumed downstream without re-derivation.

Structured contract copied for validation or lookup.

Purpose

Read source-level channel, parameter, process, and test-fixture evidence before choosing Galaxy workflow inputs and outputs.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Translate Nextflow launch params, materialized inputs, sample sheets, and control flags into gxformat2-compatible Galaxy workflow inputs.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Choose Galaxy datatype extensions and confidence notes for data inputs, collection elements, and exposed outputs.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Choose Galaxy File/list/paired/list:paired/list:list interface shapes from Nextflow channel shapes.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Choose stable workflow input/output labels and promoted checkpoint outputs that future tests can address.

Trigger

When deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Pick the right sample_sheet variant and translate nf-schema column metadata into Galaxy column_definitions when the source pipeline uses sample-sheet-shaped inputs.

Trigger

When the Nextflow summary reports a samplesheetToList materialization, a parameter whose nf-schema entry sets schema: assets/schema_*.json, or a channel built from splitCsv(header: true) over a tabular params input.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Cross-check source-side reference-data classifications before translating the reference-data brief into Galaxy workflow inputs.

Trigger

When the reference-data brief is silent, low-confidence, or conflicts with source evidence for iGenomes-derived params, coordinated bundles, compute-if-missing branches, multi-DB pick-lists, or cohort-specific assets.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Translate iGenomes-style and per-asset reference-data params into Galaxy inputs without inheriting nf-core's reference-resolution magic; v1 posture is explicit optional inputs with in-tool rebuild on absence.

Trigger

When the source pipeline declares iGenomes-derived params (params.genome with getGenomeAttribute), per-asset reference path params (fasta, fasta_fai, dict, bwa_index, dbsnp, known_indels, intervals, pon), or any compute-if-missing index-building branch in the source.