Structured contract copied for validation or lookup.
- Purpose
- Read CWL step graph, edge markers, scatter, conditionals, secondary files, and tool requirements while drafting Galaxy-facing data flow.
cwl-summary-to-galaxy-data-flow
Translate a CWL summary into a Galaxy data-flow 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
8 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-data-flow
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
- Use CWL's native graph and mark only the features that need Galaxy reinterpretation.
- Verify
- Run against representative CWL summaries with scatter, secondaryFiles, and valueFrom; confirm the brief starts from summary-cwl graph edges and only adds Galaxy-specific reshape decisions.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
- Verify
- Promote after two worked CWL-to-Galaxy translations preserve this Mold boundary without moving fields.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Translate CWL arrays, records, scatter, and secondary-file shapes into Galaxy dataset and collection semantics.
- Trigger
- When CWL input/output or step wiring implies Galaxy collections, map-over, reduction, or shape changes.
Workflow-construction idiom. Usually condensed during casting.
- Purpose
- Ground collection reshape, relabel, cleanup, and map-over choices in corpus-observed Galaxy recipes.
- Trigger
- When CWL scatter, arrays, nested arrays, records, or secondary-file contracts require explicit Galaxy collection operations.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Map CWL pickValue (first_non_null / the_only_non_null / all_non_null) on workflow outputs or step inputs into Galaxy's native `pick_value` workflow module added by galaxy#22222.
- Trigger
- When any summary-cwl edge `via` contains a `pickValue:*` marker, OR any workflow_outputs[].output_source is multi-valued with pickValue, OR any steps[].in[].pick_value is non-null in the source workflow or referenced subworkflows.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Default reference for translating CWL when:/pickValue branching: pick among `paired_or_unpaired` collection input, native `pick_value` workflow step, or sibling workflows per mode.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- When the interface brief adopted a `paired_or_unpaired` shape, model inner-tool branching via `has_single_item` semantics instead of a Galaxy-level mode switch.
- Trigger
- When the preceding cwl-galaxy-interface brief uses `paired_or_unpaired` (or `list:paired_or_unpaired`) as a workflow input, OR the data-flow brief is considering it as an option.
Cast artifacts
- Claude skillcwl-summary-to-galaxy-data-flow— Translate a CWL summary into a Galaxy data-flow design brief.
Artifact handoffs
/ pipeline contractProduces
-
Reviewable Markdown brief: abstract topology, Galaxy collection semantics, placeholder transformations, unresolved Galaxy tool needs.
Consumes
-
Structured CWL summary emitted by [[summarize-cwl]]; consumed alongside the Galaxy interface brief.
-
Preceding Galaxy interface brief from [[cwl-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.
cwl-summary-to-galaxy-data-flow
Read a CWL summary plus the preceding Galaxy interface brief and emit a reviewable Markdown data-flow brief. Capture abstract topology, Galaxy collection semantics, placeholder transformations, unresolved Galaxy tool needs, confidence, and open questions.
CWL already carries structured workflow shape, so this Mold should be lighter than nextflow-summary-to-galaxy-data-flow.
Start from summary-cwl.graph.edges[] instead of rediscovering the DAG. The main work is translation pressure: CWL scatter into Galaxy map-over or collection steps, linkMerge/pickValue into explicit fan-in choices, secondary files into output contracts, and valueFrom/when into reviewable placeholders when Galaxy cannot express them directly.
Incoming References (15)
- cwl-summary-to-galaxy-templaterelated note— gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
- Cleanup, sync, and publish non-empty resultsrelated mold— Clean sparse mapped outputs, keep sibling collections aligned, then gate report publishing on non-empty results.
- Fan-in bundle, consume, and flattenrelated mold— Bundle parallel outputs into a collection consumer, then flatten nested results for pooled downstream processing.
- 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.
- Manifest to mapped collection lifecyclerelated mold— Use a manifest or table to build a collection, map a tool per row, then relabel or reshape outputs.
- Reshape, relabel, and remap by collection axisrelated mold— Use Apply Rules and deterministic relabeling when domain fan-out creates the wrong map-over axis.
- 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 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.