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freeform-summary-to-galaxy-interface

Map a free-form source summary into a Galaxy workflow interface design brief.

Mold health

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  • Source layout

    Directory Mold with only index.md 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

    4 typed references; 0 resolver issues.

  • On-demand triggers

    All on-demand references describe triggers.

  • Evidence checks

    Hypothesis references include verification.

axis
source-specific
source
freeform
name
freeform-summary-to-galaxy-interface
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.

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.
Researchgalaxy-collection-semantics

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose
Choose Galaxy collection input shapes (File / list / paired / list:paired / record) from the source's per-sample, paired, grouped, or nested data descriptions.
Trigger
When the free-form summary describes paired reads, per-sample groups, nested or grouped inputs, or any input that should become a Galaxy dataset collection.
Researchgalaxy-sample-sheet-collections

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose
Pick the right sample_sheet variant and translate described per-sample column metadata into Galaxy column_definitions when the source describes sample-sheet-shaped inputs.
Trigger
When the free-form summary describes a sample sheet, a per-sample/per-record table, or any table mapping samples to files that should become a Galaxy collection or sample-sheet input.

Cast artifacts

How to install →

Artifact handoffs

/ pipeline contract

Consumes

freeform-summary-to-galaxy-interface

Read a free-form source summary and emit a reviewable Markdown interface brief for a Galaxy workflow. Capture workflow inputs, workflow outputs, labels, Galaxy collection shapes, checkpoint outputs worth exposing for tests, source-summary provenance, confidence, and open questions.

Free-form sources are narrative- or interview-derived and carry explicit uncertainty. Translate what the summary supports into interface decisions; carry unresolved interface choices forward as open questions rather than inventing precise inputs, outputs, or labels.

The output is not a gxformat2 skeleton and not a workflow schema. It is a design handoff consumed by freeform-summary-to-galaxy-data-flow, freeform-summary-to-galaxy-template, and later test-plan work.

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 (4)