foundry-skills

Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.

Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps.

Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable.

Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan.

Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.

Convert one nf-core module directory into a Galaxy wrapper with local macros, provenance, and remote fixture-backed tests.

Translate a CWL summary into a Galaxy data-flow design brief.

Map a CWL summary into a Galaxy workflow interface design brief.

gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.

Translate CWL test fixtures into a Galaxy workflow test plan.

Resolve a CWL workflow's own declared test cases into Galaxy workflow test-data refs.

Triage failing CWL run outputs; classify failure modes; propose fixes.

Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.

Search the Tool Shed for an existing wrapper, drill from hit to a pinnable changeset, classify candidates, and recommend or fall through.

Search IWC fixtures and public sources for test data matching a data-flow shape.

Translate a free-form source summary into a CWL workflow design brief.

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

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

gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief.

Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.

Convert an abstract step into a concrete CWL CommandLineTool + step.

Assemble CWL job file(s) and expected-output assertions.

Convert an abstract step into a concrete gxformat2 step using a tool summary.

Assemble Galaxy workflow test fixtures and assertions.

Normalize a free-form user interview into the shared freeform-summary workflow handoff.

Interview a user against an existing Galaxy workflow summary and emit a reviewable, step-anchored change-set.

Apply the IWC publication checklist to an existing Galaxy workflow and emit a generalized, reviewable submission set.

Translate a Nextflow summary into a CWL data-flow design brief.

Map a Nextflow summary into a CWL Workflow interface design brief.

Translate a Nextflow summary into a Galaxy data-flow design brief.

Map a Nextflow summary into a Galaxy workflow interface design brief.

Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.

gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.

Translate Nextflow test evidence into a CWL workflow test plan.

Translate Nextflow test evidence into a Galaxy workflow test plan.

Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.

Derive workflow test inputs and expected outputs from a paper.

Path from a CWL Workflow to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the CWL → GALAXY pipeline in order, in a per-run working directory.

Apply the pinned IWC publication checklist to an existing Galaxy workflow, then validate and retest the matured result — orchestrates the Foundry skills of the GALAXY WORKFLOW MATURATION pipeline in order, in a per-run working directory.

Post-construction review journey: summarize, validate, and test an existing Galaxy workflow, then apply pinned IWC policy — orchestrates the Foundry skills of the GALAXY WORKFLOW REVIEW pipeline in order, in a per-run working directory.

Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff — orchestrates the Foundry skills of the INTERVIEW → GALAXY pipeline in order, in a per-run working directory.

Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set — orchestrates the Foundry skills of the NEXTFLOW → CWL pipeline in order, in a per-run working directory.

Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the NEXTFLOW → GALAXY pipeline in order, in a per-run working directory.

Direct path from a paper to a CWL Workflow + CommandLineTool set — orchestrates the Foundry skills of the PAPER → CWL pipeline in order, in a per-run working directory.

Direct path from a paper to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the PAPER → GALAXY pipeline in order, in a per-run working directory.

Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop — orchestrates the Foundry skills of the UPDATE-INTERVIEW → GALAXY pipeline in order, in a per-run working directory.

Re-wire a Galaxy draft region when a step's declared output can't be computed from its wired inputs.

Triage a completed or partial Foundry feedback ledger into a run review and confirmed, deduplicated upstream issue drafts.

Apply the pinned upstream IWC review policy to one Galaxy workflow or pull request and emit one evidenced advisory Markdown review.

Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.