Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Use the gxformat2 structural vocabulary for workflow inputs, outputs, steps, and producer-side output actions while emitting the skeleton.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Emit the gxformat2 draft superset: TODO tool_id, optional tool_state / tool_shed_repository, and per-step _plan_state / _plan_context planning fields.

Verify

Promote after a downstream per-step implementation Mold consumes _plan_state and _plan_context without round-tripping back through the source summary.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Choose stable workflow input/output labels, testable checkpoint outputs, and fixture-compatible workflow interfaces while drafting the skeleton.

Trigger

When the template decides workflow inputs, workflow outputs, promoted checkpoints, or collection output identifiers that future tests will need to address.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Preserve Galaxy collection typing and map-over/reduction semantics in the gxformat2 skeleton.

Trigger

When creating workflow inputs, outputs, and placeholder connections involving collections.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Respect the handoff from abstract data-flow draft to gxformat2 skeleton.

Trigger

When translating abstract nodes, unresolved tool needs, and placeholder transformations into template TODOs.

Verify

Promote after two worked Nextflow-to-Galaxy templates preserve the data-flow/template split without schema changes.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Emit `when:` clauses on the right step type (subworkflow vs tool) and the right output fan-in primitive (`pick_value`, modes `first_non_null` / `first_or_skip` / `the_only_non_null`) when the data-flow brief carries a conditional disposition through to the skeleton.

Trigger

When the upstream data-flow brief assigns a source conditional to a subworkflow `when:` or inline `when:` shape, or when emitting the merge step for two or more `when:`-gated branches that produce the same logical output.

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose

Cross-check source-side reference-data classifications before committing reference assets, optional inputs, and rebuild behavior into the gxformat2 skeleton.

Trigger

When emitting workflow inputs or input-connection wiring for reference assets and 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

Resolve reference-asset declarations into gxformat2 inputs with the right datatype, optionality, and rebuild-on-absence wiring; cross-check the upstream brief against the datatypes table and v1 posture when the brief is silent or low-confidence on a specific asset.

Trigger

When emitting workflow inputs or input-connection wiring for any reference asset flagged in the reference-data brief (FASTA, fai, dict, indexes, dbsnp, known_indels, intervals, PoN, …), or when the source pipeline declares iGenomes-derived params, per-asset reference path params, or any compute-if-missing index-building branch.