Structured contract copied for validation or lookup.
- Purpose
- Read CWL workflow inputs, outputs, types, formats, secondary files, scatter, and requirement evidence before choosing the Galaxy interface.
cwl-summary-to-galaxy-interface
Map a CWL summary into a Galaxy workflow interface design brief.
Mold health
ok- Source layout
Directory Mold with only index.md frontmatter.
- Axis fields
source-specific fields are coherent.
- Eval plan
eval.md declares cases and check type.
- Typed refs
6 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 Mold references describe what casting consumes and when the generated skill should load each artifact.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Choose stable Galaxy workflow input/output labels and promoted checkpoint outputs.
- Trigger
- When deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Pick among the three honest Galaxy branching translations (paired_or_unpaired input, native pick_value step, sibling workflows) before drafting the interface.
- Trigger
- When summary-cwl has any steps[].when non-null OR any workflow output uses pickValue.
Cast artifacts
- Claude skillcwl-summary-to-galaxy-interface— Map a CWL summary into a Galaxy workflow interface design brief.
Artifact handoffs
/ pipeline contractProduces
-
Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, exposed and checkpoint outputs, source provenance, confidence.
Consumes
-
Structured CWL summary emitted by [[summarize-cwl]]; the source-of-truth JSON for Galaxy interface choices.
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-flowrelated note— Translate a CWL summary into a Galaxy data-flow design brief.
- cwl-summary-to-galaxy-templaterelated note— gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
- CWL → GALAXYphase of pipeline— Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.
- CWL workflow anatomyrelated mold— CWL structure relevant to summarize-cwl: normalized documents, steps, scatter, conditionals, requirements, and dependency handling.
- CWL when:/pickValue → Galaxy branching translationrelated 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 typerelated 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 summaryrelated note— JSON Schema for the structured summary emitted by the summarize-cwl Mold.