paper-summary-to-galaxy-design

Translate a paper summary into a Galaxy workflow design brief.

Mold health

warn

Source layout
Directory Mold with only index.md frontmatter.
Axis fields
source-specific fields are coherent.
Eval plan
eval.md not written yet.
Typed refs
1 typed reference; 0 resolver issues.
On-demand triggers
All on-demand references describe triggers.
Evidence checks
Hypothesis references include verification.

axis: source-specific
source: paper
name: paper-summary-to-galaxy-design

contract

Reference Loading

Typed Mold references describe what casting consumes and when the generated skill should load each artifact.

Researchgalaxy-data-flow-draft-contract

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Hypothesis

Purpose: Use the same Galaxy design-brief boundary without forcing paper-derived evidence into a source-summary schema.
Trigger: When paper extraction has enough workflow structure to draft Galaxy interface and data-flow decisions.
Verify: Promote after two worked paper-to-Galaxy translations show the combined design brief is enough context for template generation.

Artifact handoffs

/ pipeline contract

Produces

paper-galaxy-design markdown paper-galaxy-design.md

Combined Galaxy interface + data-flow design brief; a single reviewable handoff until paper examples justify a split.
consumed by
- compare-against-iwc-exemplar
- paper-summary-to-galaxy-template

Consumes

summary-paper

Paper extraction emitted by [[summarize-paper]]; methods, tools, sample data, references.
produced by
- summarize-paper

paper-summary-to-galaxy-design

Read a paper summary and emit a reviewable Markdown Galaxy workflow design brief. Combine interface choices and abstract data-flow choices until paper examples justify a cleaner split.

The output is not gxformat2 and not a rich workflow schema. paper-summary-to-galaxy-template turns this brief and the paper summary into a skeleton.

Incoming References (3)

paper-summary-to-galaxy-templaterelated note— gxformat2 skeleton with per-step TODOs from a paper summary and the paper-to-Galaxy design brief.
PAPER → GALAXYphase of pipeline— Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.
Galaxy data-flow draft contractrelated mold— Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.