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cwl-summary-to-galaxy-data-flow

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

draft moldsource/cwltarget/galaxy
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Mold health

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  • Source layout

    1 non-index Markdown file with frontmatter.

  • Axis fields

    source-specific fields are coherent.

  • Eval plan

    Abstract oracle: fixture-independent property checks any run must satisfy.

    eval.md declares properties and check type.

    eval.md ↗
  • Scenarios

    Concrete cases: fixtures bound to expected values, 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 Mold references describe what casting consumes and when the generated skill should load each artifact.

Researchopen-requirements-ledger

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeUpfrontVerbatimHypothesis
Purpose
Carry the open-requirements ledger: read open entries bearing on this step's decisions, mark resolved the ones it closes, and append any new unmet need it surfaces.
Verify
Promote after a worked run shows entries this Mold appends or resolves are consumed downstream without re-derivation.
Researchcomponent-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.
Researchgalaxy-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.
Patterngalaxy-collection-patterns

Workflow-construction idiom. Usually condensed during casting.

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.
Patterngalaxy-conditionals-patterns

Workflow-construction idiom. Usually condensed during casting.

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.
Patterngalaxy-interval-patterns

Workflow-construction idiom. Usually condensed during casting.

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.
Researchcwl-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.
Researchgalaxy-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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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.

Carry the open-requirements-ledger through this step: read the open entries that bear on the choices you make here, mark resolved any your decisions close, and append any new unmet need you surface — a declared output with no producer, an unpinned parameter, a tool with no corpus exemplar — so a later Mold inherits it instead of re-deriving it.

Incoming References (17)