Home Mold

freeform-summary-to-galaxy-data-flow

Translate a free-form source summary into a Galaxy data-flow design brief.

reviewed source/freeform target/galaxy

Related: freeform-summary-to-galaxy-interface
freeform-summary-to-galaxy-template

Mold health

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
7 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-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.

Runtime Upfront Verbatim Hypothesis

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 narrative leaves open — a described transformation with no named tool, an implied intermediate the source never states, an ordering the prose doesn't fix.
Verify: Promote after a worked run shows entries this Mold appends or resolves are consumed downstream without re-derivation.

Research galaxy-data-flow-draft-contract

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Hypothesis

Purpose: Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
Verify: Promote after two worked freeform-to-Galaxy translations preserve this Mold boundary without moving fields.

Pattern galaxy-collection-patterns

Workflow-construction idiom. Copied verbatim.

Runtime On Demand Verbatim Corpus Observed

Purpose: Ground collection-shape choices in curated, corpus-observed operation and recipe patterns.
Trigger: When selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.

Pattern galaxy-tabular-patterns

Workflow-construction idiom. Copied verbatim.

Runtime On Demand Verbatim Corpus Observed

Purpose: Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns.
Trigger: When data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.

Pattern galaxy-conditionals-patterns

Workflow-construction idiom. Copied verbatim.

Runtime On Demand Verbatim Corpus 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.

Runtime On Demand Verbatim Corpus 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 galaxy-sample-sheet-collections

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it.
Trigger: When the interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or the free-form summary describes per-sample/per-record metadata that must survive map-over steps.

Cast artifacts

Claude skill freeform-summary-to-galaxy-data-flow — Translate a free-form source summary into a Galaxy data-flow design brief.

How to install →

Artifact handoffs

/ pipeline contract

Produces

freeform-galaxy-data-flow markdown freeform-galaxy-data-flow.md

Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions.
consumed by
open-requirements-ledger yaml open-requirements.ledger.yml

Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.
consumed by

Consumes

freeform-summary

Free-form source summary emitted by [[summarize-paper]] or [[interview-to-freeform-summary]]; consumed alongside the Galaxy interface brief.
produced by
- interview-to-freeform-summary
- summarize-paper
freeform-galaxy-interface

Preceding Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.
produced by
- freeform-summary-to-galaxy-interface
open-requirements-ledger

Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.
produced by

freeform-summary-to-galaxy-data-flow

Read a free-form source summary plus the preceding Galaxy interface brief and emit a reviewable Markdown data-flow brief. Capture abstract operations, collection map/reduce choices, shape-changing placeholder transformations, unresolved Galaxy tool needs, confidence, and open questions.

Free-form sources rarely give enough to fix exact operations. Translate what the summary and interface brief support, classify the rest as unresolved tool needs or open questions, and do not present narrative intent as already-decided Galaxy wiring.

The output is not gxformat2 and should not resolve exact Tool Shed tools. freeform-summary-to-galaxy-template turns this handoff and the interface brief into a skeleton.

Incoming References (5)

freeform-summary-to-galaxy-interface related note — Map a free-form source summary into a Galaxy workflow interface design brief.
freeform-summary-to-galaxy-template related note — gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief.
INTERVIEW → GALAXY phase of pipeline — Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff.
PAPER → GALAXY phase of pipeline — Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.
Galaxy data-flow draft contract related mold — Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.