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cwl-summary-to-galaxy-data-flow

Translate a CWL summary into a Galaxy data-flow design brief.

draft source/cwltarget/galaxy
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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

    11 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 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 wiring and collection decisions settle, and append data-flow obligations the CWL summary can't settle — a scatter shape Galaxy can't express directly, an expression-derived value with no Galaxy equivalent, a `linkMerge`/`pickValue` fan-in with no settled Galaxy form.
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
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.
Research galaxy-data-flow-draft-contract

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeUpfrontVerbatimHypothesis
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.
Research galaxy-collection-semantics

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
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.
Pattern galaxy-collection-patterns

Workflow-construction idiom. Copied verbatim.

RuntimeOn DemandVerbatimCorpus Observed
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.
Pattern galaxy-conditionals-patterns

Workflow-construction idiom. Copied verbatim.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns.
Trigger
When data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.
Pattern galaxy-interval-patterns

Workflow-construction idiom. Copied verbatim.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes.
Trigger
When the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.
Research cwl-pickvalue-to-galaxy

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
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.
Research galaxy-paired-or-unpaired-collections

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
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

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Artifact handoffs

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Produces

Consumes

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 (17)