Structured contract copied for validation or lookup.
- Purpose
- Read CWL source graph, step ids, command surfaces, scatter, conditionals, requirements, and warnings while emitting placeholder steps.
cwl-summary-to-galaxy-template
gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
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
9 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-template
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
- Preserve the lightweight CWL boundary and avoid re-inferring structure already present in the summary.
- Verify
- Run after the first CWL interface/data-flow briefs and confirm gxformat2 placeholder steps preserve CWL step boundaries unless the data-flow brief explicitly asks to split them.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Use the gxformat2 structural vocabulary for workflow inputs, outputs, steps, and placeholder wiring.
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
- Translate CWL arrays, records, scatter, and secondary-file shapes into Galaxy collection typing and map-over/reduction semantics.
- 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 CWL-to-Galaxy templates preserve the data-flow/template split without schema changes.
Workflow-construction idiom. Usually condensed during casting.
- Purpose
- Use corpus-grounded collection pattern guidance for unresolved skeleton steps.
- Trigger
- When adding TODO steps for collection cleanup, reshaping, relabeling, identifier synchronization, or collection-tabular bridges.
Workflow-construction idiom. Usually condensed during casting.
- Purpose
- Use corpus-grounded tabular pattern guidance for unresolved skeleton steps.
- Trigger
- When adding TODO steps for tabular filtering, projection, joins, aggregation, text-processing recipes, or tabular-collection bridges.
Cast artifacts
- Claude skillcwl-summary-to-galaxy-template— gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
Artifact handoffs
/ pipeline contractProduces
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gxformat2 draft (see [[galaxy-workflow-draft-format]]): topology fully resolved (workflow inputs, outputs, step set, edges); tool_id / tool_state / tool_shed_repository and wrapper-determined port names may be TODO with free-text _plan_state / _plan_context / _plan_in / _plan_out per step for later implementation Molds.
Consumes
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Structured CWL summary emitted by [[summarize-cwl]]; consulted while emitting placeholder steps.
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Galaxy interface brief from [[cwl-summary-to-galaxy-interface]] that pins workflow inputs, outputs, labels.
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Galaxy data-flow brief from [[cwl-summary-to-galaxy-data-flow]] that pins abstract operations and collection choices.
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Structural diff guidance from [[compare-against-iwc-exemplar]] (run on the design briefs); steers the skeleton toward IWC-aligned structure before per-step authoring.
cwl-summary-to-galaxy-template
Read the original CWL source artifact, the CWL summary, the CWL-to-Galaxy interface brief, and the CWL-to-Galaxy data-flow brief. Emit a gxformat2 skeleton with workflow inputs, workflow outputs, placeholder steps, rough connections, and TODO slots for later implementation Molds.
CWL already carries structured workflow shape, so this Mold should be lighter than nextflow-summary-to-galaxy-template. Treat the prior-step index as the working context: CWL source, CWL summary, interface brief, data-flow brief, and any open questions carried forward.
Topology is this Mold’s job to settle. The output must be concrete gxformat2: workflow inputs with their final collection shapes and formats, workflow outputs, the step set, the producer→consumer edge graph, branches, and when: guards are all decided here. The upstream interface and data-flow briefs guide those decisions, but if they hedge or leave a topology choice open, this Mold makes the call from source evidence, IWC exemplars, and pattern pages — never emit a topology TODO. What is deferred to per-step authoring is strictly wrapper-tier: tool_id, tool_version, tool_shed_repository, tool_state, and the wrapper-determined port names that surface in in: / out: / outputSource. Capture deferred intent in the _plan_* family (_plan_state, _plan_context, _plan_in, _plan_out) so the per-step Mold has the source evidence and constraints it needs.
Defer thoughtfully. When research surfaces a Foundry pattern page that names the exact recipe — a galaxy-collection-patterns reshape, a conditional-run-optional-step gate, a galaxy-tabular-patterns filter — fill the step in as completely as the pattern allows: concrete tool_id, parameters, port names from the pattern’s worked example. Pattern pages encode resolved choices; emitting TODO over a covered recipe discards real evidence the per-step Mold cannot recover. Defer only when the step is a domain-specific CWL CommandLineTool with no covering pattern, and pack _plan_context with the baseCommand / arguments, DockerRequirement URIs, SoftwareRequirement packages, and EnvVarRequirement / ResourceRequirement constraints the per-step Mold needs to pick a wrapper.
Output shape is gxformat2 with wrapper-tier relaxations and _plan_state / _plan_context / _plan_in / _plan_out per tool step — see galaxy-workflow-draft-format. Refinement open work for those planning fields lives in refinement.md.
Use CWL step ids as the first pass for placeholder labels, then revise labels only when the interface/data-flow briefs or IWC comparison notes give a clearer Galaxy convention. Preserve one placeholder per logical CWL step unless the data-flow brief explicitly asks to split an expression, nested workflow, or collection operation into Galaxy-native steps.
Incoming References (10)
- Galaxy: collection patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy collection transformation patterns.
- Galaxy: conditionals patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns.
- Galaxy: tabular patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
- 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 pickValue → Galaxy pick_value (post galaxy#22222)related mold— CWL `pickValue` (first_non_null / the_only_non_null / all_non_null) → Galaxy's native `pick_value` workflow step added by galaxyproject/galaxy#22222.
- 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 data-flow draft contractrelated mold— Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.
- Galaxy workflow draft formatrelated mold— gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step.
- CWL workflow summaryrelated note— JSON Schema for the structured summary emitted by the summarize-cwl Mold.