Structured contract copied for validation or lookup.
- Purpose
- Read and validate the structured source evidence without turning its processes or containers into Galaxy choices.
nextflow-summary-to-workflow-brief
Turn a nextflow source summary and selected scope into a Workflow Brief without Galaxy design assumptions.
Mold health
ok- 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
5 typed references; 0 resolver issues.
- On-demand triggers
All on-demand references describe triggers.
- Evidence checks
Hypothesis references include verification.
- axis
- source-specific
- source
- nextflow
- name
- nextflow-summary-to-workflow-brief
contract
Reference Loading
Typed references describe what casting consumes, and when the generated skill should load each artifact.
Structured contract copied for validation or lookup.
- Purpose
- Carry the Markdown section declaration and its structural validator.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Apply the brief boundaries: evidence and expert intent, no inferred Galaxy design, and separate workflow/environment blockers.
- Verify
- Check the committed fixtures and review a worked run for faithful evidence and unchanged brief input.
Command reference. Usually cast to a sidecar and loaded only when invoked.
- Purpose
- Validate the emitted brief before returning it.
- Trigger
- After writing workflow-brief.md.
- Verify
- Check the committed fixtures and review a worked run for faithful evidence and unchanged brief input.
Command reference. Usually cast to a sidecar and loaded only when invoked.
- Purpose
- Report declared blockers separately from structural validity.
- Trigger
- After structural validation and before reporting whether the brief is clear of declared blockers.
- Verify
- Check the committed fixtures and review a worked run for faithful evidence and unchanged brief input.
Cast artifacts
- Claude skill nextflow-summary-to-workflow-brief — Turn a nextflow source summary and selected scope into a Workflow Brief without Galaxy design assumptions.
Artifact handoffs
/ pipeline contractProduces
-
Expert-editable workflow intent and agent environment, with optional details and explicit workflow or environment blockers.
Consumes
-
Source evidence supplied by the preceding summarizer; preserve uncertainty and the caller’s selected scope.
nextflow-summary-to-workflow-brief
Read the structured summary-nextflow and the caller’s selected scientific scope, then emit a Workflow Brief for expert review.
Record the selected analyses and source pin. Keep process topology, source container references, parameter evidence, reference assets, and test candidates in the linked source summary. A Nextflow process is not evidence of an available Galaxy wrapper or of a required Galaxy step.
Evidence and scope
Read the source summary and the caller’s stated objective and selection. Identify which scientific work is included and excluded; do not copy every source analysis into scope. If the selection is too ambiguous to proceed, state that uncertainty explicitly in Workflow/Blockers rather than choosing an analysis for the expert.
Write workflow-brief.md with ## Workflow, ### Objective, and ## Agent Environment. Add optional subsections only when evidence or expert intent supports them. Identify the source and caller instructions, distinguish source facts from expert requirements, and keep scientific inputs, outputs, and acceptance criteria high-level. Missing optional detail does not require filler sections.
The writing agent must not infer Galaxy datatypes, collections, interface labels, available tools, or wrapper versions. It must not write step graphs, concrete tool states, or final test declarations. Named source tools and formats are evidence, not Galaxy choices. Explicit expert-provided Galaxy requirements may be recorded with attribution.
Agent environment
Use supplied environment evidence or harmless availability/version probes to describe expected gxwf, foundry, and planemo tooling, agent constraints, container preferences, and Docker/Singularity/Apptainer usability. Distinguish requested requirements, observed facts, and unknowns. Do not claim a container engine works based only on an executable being on PATH. Do not install tools or change the environment as part of brief production.
Place known issues preventing work in ### Blockers under the appropriate parent. Put nonblocking questions in Workflow/Open questions. Omit or leave Blockers empty when there are none; any text there, including “none”, is blocking.
Validate and hand off
Run foundry validate-workflow-brief workflow-brief.md. Fix structural failures without inventing scientific intent. Run foundry check-workflow-brief workflow-brief.md --json and retain its result in the run report. Exit 4 means a valid but blocked brief: return that brief and its blockers for expert/environment resolution. Do not suppress the blockers to obtain a clear check.
Return the brief for expert editing and review. Producing a brief does not authorize Galaxy design or implementation, and a clear static check does not replace review or environment preflight. Keep source evidence available to the later consumer.
Incoming References (1)
- NEXTFLOW → WORKFLOW BRIEF phase of pipeline — Summarize a Nextflow pipeline and produce a scoped Workflow Brief for expert review.