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cwl-summary-to-galaxy-interface

Map a CWL summary into a Galaxy workflow interface design brief.

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  • Source layout

    Every file beside index.md is one the mold kind declares.

  • Axis fields

    source-specific fields are coherent.

  • Eval plan

    Abstract oracle: the properties any cast of this Mold must satisfy.

    eval.md declares properties and check type.

    eval.md ↗
  • Scenarios

    Concrete cases bound to fixtures, run against the eval properties.

    scenarios.md declares cases bound to fixtures.

    scenarios.md ↗
  • Typed refs

    7 typed references; 0 resolver issues.

  • On-demand triggers

    All on-demand references describe triggers.

  • Evidence checks

    Hypothesis references include verification.

axis
source-specific
source
cwl
name
cwl-summary-to-galaxy-interface
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Research open-requirements-ledger

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeUpfrontVerbatimHypothesis
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 CWL summary leaves open — an unmapped secondaryFiles bundle, an unpinned parameter default, a collection shape the source types don't determine.
Verify
Promote after a worked run shows entries this Mold appends or resolves are consumed downstream without re-derivation.
Research component-cwl-workflow-anatomy

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeUpfrontVerbatimHypothesis
Purpose
Keep source-faithful CWL facts separate from Galaxy-facing interface choices.
Verify
Run against the first representative CWL summaries and confirm workflow inputs/outputs map without re-parsing the original CWL.
Research galaxy-collection-semantics

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Choose Galaxy collection input shapes from CWL arrays, scatter inputs, records, Directory values, and secondary-file contracts.
Trigger
When CWL types include arrays, records, Directory, secondaryFiles, or scatter over File-like inputs.
Research galaxy-paired-or-unpaired-collections

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Choose `paired_or_unpaired` (or `list:paired_or_unpaired`) shape when the CWL discriminator is paired-vs-single reads, instead of inventing a workflow-level `reads_mode` select parameter.
Trigger
When summary-cwl declares 2+ optional File? read-like inputs whose step bindings are gated by complementary `when:` predicates, OR workflow outputs use pickValue over branches keyed on input presence, OR an upstream `meta.single_end`-style discriminator surfaces in the summary.

Cast artifacts

How to install →

Artifact handoffs

/ pipeline contract

Produces

Consumes

cwl-summary-to-galaxy-interface

Read a CWL summary and emit a reviewable Markdown interface brief for a Galaxy workflow. Preserve CWL input/output intent while choosing Galaxy-facing labels, data shapes, exposed outputs, checkpoint outputs, provenance, confidence, and open questions.

The output is a design handoff, not gxformat2 and not a rich workflow schema.

Prefer direct mappings when they are honest: CWL scalar inputs become Galaxy parameter inputs, File inputs become dataset inputs, File[] plus scatter commonly becomes a list collection, and declared formats seed Galaxy datatype choices. Surface Directory, records, expression-shaped defaults, and secondary-file-heavy outputs as review notes rather than flattening them silently.

Incoming References (7)

  • cwl-summary-to-galaxy-data-flow related note — Translate a CWL summary into a Galaxy data-flow design brief.
  • cwl-summary-to-galaxy-template related note — gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
  • CWL → GALAXY phase of pipeline — Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.
  • CWL workflow anatomy related mold — CWL structure relevant to summarize-cwl: normalized documents, steps, scatter, conditionals, requirements, and dependency handling.
  • CWL when:/pickValue → Galaxy branching translation related mold — CWL `when:`/`pickValue` → Galaxy. Three honest translations (paired_or_unpaired input, native pick_value step, sibling workflows) plus how to pick among them.
  • Galaxy paired_or_unpaired collection type related mold — Galaxy's `paired_or_unpaired` collection type: discriminated-union shape for paired-or-single reads, no workflow-level mode switch needed. Galaxy PR #19377.
  • CWL workflow summary related note — JSON Schema for the structured summary emitted by the summarize-cwl Mold.