foundry

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.

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

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

Assemble Galaxy workflow test fixtures and assertions.

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

Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).

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.

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.

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

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 Galaxy workflow test plan.

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

Read a Nextflow pipeline source tree (nf-core or ad-hoc DSL2) and emit a structured JSON summary for downstream translation Molds.

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.

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

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

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

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

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

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

Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps.

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

Validate and normalize a CWL Workflow tree, then emit a lightweight structured summary for downstream Galaxy translation.

Pull JSON schema, container, source, inputs/outputs for a Galaxy tool.

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

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

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

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

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

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

Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.