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freeform-summary-to-galaxy-data-flow

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

draft moldsource/freeformtarget/galaxy
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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

    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 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.
Researchgalaxy-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 freeform-to-Galaxy translations preserve this Mold boundary without moving fields.
Patterngalaxy-tabular-patterns

Workflow-construction idiom. Usually condensed during casting.

RuntimeOn DemandVerbatimCorpus 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.
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.
Researchgalaxy-sample-sheet-collections

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus 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

How to install →

Artifact handoffs

/ pipeline contract

Produces

Consumes

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.

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 (5)