Usage

Choose a route. Install once. Run the work.

The Foundry casts each Mold into a self-contained skill, and assembles each Pipeline into a runnable harness. Both are committed under casts/ and surfaced as one shared Agent Skills bundle with thin Claude Code, Codex, and Antigravity plugin metadata. Install once in your runtime, then choose a Direct Build, a Plan & Build route with an expert-review boundary, or an existing Galaxy workflow task. You can also invoke any cast skill directly.

Pipelines: 13
Shared skills: 56
Casts: 56

Install

/ one bundle, three runtimes

Claude Code. Add the marketplace and install the plugin:

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Skills are namespaced under the plugin. Invoke a cast skill in a session like:

/foundry-skills:summarize-nextflow

Codex. Add the same repository marketplace and install the same plugin:

codex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundry

In Codex CLI or the IDE, run /skills or type $ to select a skill explicitly:

$summarize-nextflow

Codex may also select a skill implicitly when your task matches its description.

Antigravity. Install the plugin using the agy CLI:

git clone https://github.com/galaxyproject/foundry
agy plugin install foundry/casts/claude

In Antigravity CLI (agy) or the IDE, run /skills to list skills, or invoke directly with slash commands:

/summarize-nextflow

Antigravity also discovers workspace customizations automatically via .agents/skills.json or .agents/plugins.json when working inside the repository clone, or selects skills progressively based on task descriptions.

Or skip plugin installation and copy a single skill into the runtime's user skill directory:

git clone https://github.com/galaxyproject/foundry
cp -r foundry/casts/claude/skills/<name> ~/.claude/skills/<name>        # Claude Code
cp -r foundry/casts/claude/skills/<name> ~/.agents/skills/<name>        # Codex
cp -r foundry/casts/claude/skills/<name> ~/.gemini/config/skills/<name> # Antigravity

Update Claude Code with /plugin update foundry-skills@galaxy-workflow-foundry. Refresh the Codex marketplace with codex plugin marketplace upgrade galaxy-workflow-foundry. Update Antigravity by pulling latest and re-running agy plugin install foundry/casts/claude. Restart the runtime if updated skills do not appear.

Run a pipeline

/ choose the route that matches the work

Each command invokes an assembled pipeline-* harness. Direct Build keeps source-to-target work in one pipeline. Plan & Build makes the Workflow Brief — and its expert-review boundary — explicit. Either route can still pause for expert input or stop on blockers.

Install the harness skills. They install through the Claude Code, Codex, or Antigravity plugin metadata around the same shared bundle. See Install.
Make the runtime available. Pipelines call out to gxwf, Planemo, and the Foundry validators when their phases require them.
Invoke a harness below. Every run gets its own ./<run-slug>/ working directory, keeping artifacts isolated.
Optional flags. Use --use-subagents to isolate phase context and --checkpoint to commit the run directory after each phase.

Direct Build

Use one pipeline when you do not need a separate, reviewable planning artifact.

6 routes

pipeline-cwl-to-galaxy CWL → GALAXY

Translate a CWL Workflow into a Galaxy gxformat2 workflow, then assemble and run a Galaxy workflow test.
12 phases · 11 auto · 1 manual · 1 loop
```
Claude:      /foundry-skills:pipeline-cwl-to-galaxy
Codex:       $pipeline-cwl-to-galaxy
Antigravity: /pipeline-cwl-to-galaxy
```
pipeline-interview-to-galaxy INTERVIEW → GALAXY

Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff.
12 phases · 11 auto · 1 manual · 1 loop
```
Claude:      /foundry-skills:pipeline-interview-to-galaxy
Codex:       $pipeline-interview-to-galaxy
Antigravity: /pipeline-interview-to-galaxy
```
pipeline-nextflow-to-cwl NEXTFLOW → CWL

Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set.
12 phases · 12 auto · 0 manual · 3 loops
```
Claude:      /foundry-skills:pipeline-nextflow-to-cwl
Codex:       $pipeline-nextflow-to-cwl
Antigravity: /pipeline-nextflow-to-cwl
```
pipeline-nextflow-to-galaxy NEXTFLOW → GALAXY

Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
13 phases · 12 auto · 1 manual · 1 loop
```
Claude:      /foundry-skills:pipeline-nextflow-to-galaxy
Codex:       $pipeline-nextflow-to-galaxy
Antigravity: /pipeline-nextflow-to-galaxy
```
pipeline-paper-to-cwl PAPER → CWL

Direct path from a paper to a CWL Workflow + CommandLineTool set.
11 phases · 10 auto · 1 manual · 3 loops
```
Claude:      /foundry-skills:pipeline-paper-to-cwl
Codex:       $pipeline-paper-to-cwl
Antigravity: /pipeline-paper-to-cwl
```
pipeline-paper-to-galaxy PAPER → GALAXY

Direct path from a paper to a Galaxy gxformat2 workflow. No Workflow Brief or CWL intermediate.
12 phases · 11 auto · 1 manual · 1 loop
```
Claude:      /foundry-skills:pipeline-paper-to-galaxy
Codex:       $pipeline-paper-to-galaxy
Antigravity: /pipeline-paper-to-galaxy
```

Plan & Build

Split planning from implementation when the decisions deserve explicit expert review.

2 pipeline stages

Create a Workflow BriefChoose the source-specific planner.

pipeline-interview-to-workflow-brief INTERVIEW → WORKFLOW BRIEF

Summarize an interview source and produce a scoped Workflow Brief for expert review.
2 phases · 2 auto · 0 manual
```
Claude:      /foundry-skills:pipeline-interview-to-workflow-brief
Codex:       $pipeline-interview-to-workflow-brief
Antigravity: /pipeline-interview-to-workflow-brief
```
pipeline-nextflow-to-workflow-brief NEXTFLOW → WORKFLOW BRIEF

Summarize a Nextflow pipeline and produce a scoped Workflow Brief for expert review.
2 phases · 2 auto · 0 manual
```
Claude:      /foundry-skills:pipeline-nextflow-to-workflow-brief
Codex:       $pipeline-nextflow-to-workflow-brief
Antigravity: /pipeline-nextflow-to-workflow-brief
```
pipeline-paper-to-workflow-brief PAPER → WORKFLOW BRIEF

Summarize a paper source and produce a scoped Workflow Brief for expert review.
2 phases · 2 auto · 0 manual
```
Claude:      /foundry-skills:pipeline-paper-to-workflow-brief
Codex:       $pipeline-paper-to-workflow-brief
Antigravity: /pipeline-paper-to-workflow-brief
```

Expert review & edit Inspect the brief, resolve blockers, and revise it before implementation.

Build from the Workflow BriefRun the agreed plan through Galaxy implementation.

pipeline-workflow-brief-to-galaxy WORKFLOW BRIEF → GALAXY

Consume an expert-reviewed, unchanged Workflow Brief directly through the Galaxy design and implementation chain.
11 phases · 10 auto · 1 manual · 1 loop
```
Claude:      /foundry-skills:pipeline-workflow-brief-to-galaxy
Codex:       $pipeline-workflow-brief-to-galaxy
Antigravity: /pipeline-workflow-brief-to-galaxy
```

Existing Galaxy workflows

Review, mature, or update a workflow that already exists.

3 routes

pipeline-galaxy-workflow-maturation GALAXY WORKFLOW MATURATION

Apply the pinned IWC publication checklist to an existing Galaxy workflow, then validate and retest the matured result.
4 phases · 4 auto · 0 manual
```
Claude:      /foundry-skills:pipeline-galaxy-workflow-maturation
Codex:       $pipeline-galaxy-workflow-maturation
Antigravity: /pipeline-galaxy-workflow-maturation
```
pipeline-galaxy-workflow-review GALAXY WORKFLOW REVIEW

Post-construction review journey: summarize, validate, and test an existing Galaxy workflow, then apply pinned IWC policy.
4 phases · 4 auto · 0 manual
```
Claude:      /foundry-skills:pipeline-galaxy-workflow-review
Codex:       $pipeline-galaxy-workflow-review
Antigravity: /pipeline-galaxy-workflow-review
```
pipeline-update-interview-to-galaxy UPDATE-INTERVIEW → GALAXY

Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop.
9 phases · 9 auto · 0 manual · 1 loop
```
Claude:      /foundry-skills:pipeline-update-interview-to-galaxy
Codex:       $pipeline-update-interview-to-galaxy
Antigravity: /pipeline-update-interview-to-galaxy
```

Shared Agent Skills

/ 56 casts

advance-galaxy-draft-step Source mold →

Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
apply-galaxy-workflow-changeset Source mold →

Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps.
author-galaxy-tool-wrapper Source mold →

Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable.
changeset-to-galaxy-test-plan Source mold →

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.
compare-against-iwc-exemplar Source mold →

Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.
convert-nfcore-module-to-galaxy-tool Source mold →

Convert one nf-core module directory into a Galaxy wrapper with local macros, provenance, and remote fixture-backed tests.
cwl-summary-to-galaxy-data-flow Source mold →

Translate a CWL summary into a Galaxy data-flow design brief.
cwl-summary-to-galaxy-interface Source mold →

Map a CWL summary into a Galaxy workflow interface design brief.
cwl-summary-to-galaxy-template Source mold →

gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
cwl-test-to-galaxy-test-plan Source mold →

Translate CWL test fixtures into a Galaxy workflow test plan.
cwl-to-test-data Source mold →

Resolve a CWL workflow's own declared test cases into Galaxy workflow test-data refs.
debug-cwl-workflow-output Source mold →

Triage failing CWL run outputs; classify failure modes; propose fixes.
debug-galaxy-workflow-output Source mold →

Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
discover-shed-tool Source mold →

Search the Tool Shed for an existing wrapper, drill from hit to a pinnable changeset, classify candidates, and recommend or fall through.
find-test-data Source mold →

Search IWC fixtures and public sources for test data matching a data-flow shape.
freeform-summary-to-cwl-design Source mold →

Translate a free-form source summary into a CWL workflow design brief.
freeform-summary-to-galaxy-data-flow Source mold →

Translate a free-form source summary into a Galaxy data-flow design brief.
freeform-summary-to-galaxy-interface Source mold →

Map a free-form source summary into a Galaxy workflow interface design brief.
freeform-summary-to-galaxy-template Source mold →

gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief.
freeform-summary-to-galaxy-test-plan Source mold →

Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
freeform-summary-to-workflow-brief Source mold →

Turn a freeform source summary and selected scope into a Workflow Brief without Galaxy design assumptions.
implement-cwl-tool-step Source mold →

Convert an abstract step into a concrete CWL CommandLineTool + step.
implement-cwl-workflow-test Source mold →

Assemble CWL job file(s) and expected-output assertions.
implement-galaxy-tool-step Source mold →

Convert an abstract step into a concrete gxformat2 step using a tool summary.
implement-galaxy-workflow-test Source mold →

Assemble Galaxy workflow test fixtures and assertions.
interview-to-freeform-summary Source mold →

Normalize a free-form user interview into the shared freeform-summary workflow handoff.
interview-to-galaxy-workflow-changeset Source mold →

Interview a user against an existing Galaxy workflow summary and emit a reviewable, step-anchored change-set.
mature-galaxy-workflow-for-iwc Source mold →

Apply the IWC publication checklist to an existing Galaxy workflow and emit a generalized, reviewable submission set.
nextflow-summary-to-cwl-data-flow Source mold →

Translate a Nextflow summary into a CWL data-flow design brief.
nextflow-summary-to-cwl-interface Source mold →

Map a Nextflow summary into a CWL Workflow interface design brief.
nextflow-summary-to-galaxy-data-flow Source mold →

Translate a Nextflow summary into a Galaxy data-flow design brief.
nextflow-summary-to-galaxy-interface Source mold →

Map a Nextflow summary into a Galaxy workflow interface design brief.
nextflow-summary-to-galaxy-reference-data Source mold →

Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.
nextflow-summary-to-galaxy-template Source mold →

gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.
nextflow-summary-to-workflow-brief Source mold →

Turn a nextflow source summary and selected scope into a Workflow Brief without Galaxy design assumptions.
nextflow-test-to-cwl-test-plan Source mold →

Translate Nextflow test evidence into a CWL workflow test plan.
nextflow-test-to-galaxy-test-plan Source mold →

Translate Nextflow test evidence into a Galaxy workflow test plan.
nextflow-to-test-data Source mold →

Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.
paper-to-test-data Source mold →

Resolve the test data a paper names into refs for each workflow input.
repair-galaxy-draft-topology Source mold →

Re-wire a Galaxy draft region when a step's declared output can't be computed from its wired inputs.
report-foundry-run-feedback Source mold →

Triage a completed or partial Foundry feedback ledger into a run review and confirmed, deduplicated upstream issue drafts.
review-galaxy-workflow Source mold →

Apply the pinned upstream IWC review policy to one Galaxy workflow or pull request and emit one evidenced advisory Markdown review.
run-workflow-test Source mold →

Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
summarize-cwl Source mold →

Validate and normalize a CWL Workflow tree, then emit a lightweight structured summary for downstream Galaxy translation.
summarize-cwl-tool Source mold →

Derive a CommandLineTool description (container, baseCommand, IO) for a CWL target.
summarize-galaxy-tool Source mold →

Pull JSON schema, container, source, inputs/outputs for a Galaxy tool.
summarize-galaxy-workflow Source mold →

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

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

Extract methods, tools, sample data, and references from a paper.
summary-to-cwl-template Source mold →

CWL Workflow skeleton with per-step TODOs from source and design handoffs.
validate-cwl Source mold →

Run cwltool --validate / schema lint, classify failures, recommend fixes.
validate-galaxy-workflow Source mold →

Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.
workflow-brief-to-galaxy-data-flow Source mold →

Translate a reviewed Workflow Brief and its Galaxy interface into a Galaxy data-flow design brief.
workflow-brief-to-galaxy-interface Source mold →

Map a reviewed Workflow Brief into a Galaxy workflow interface design brief, consulting retained source evidence when available.
workflow-brief-to-galaxy-template Source mold →

Build a gxformat2 skeleton from a reviewed Workflow Brief and its Galaxy design briefs, consulting retained source evidence.
workflow-brief-to-galaxy-test-plan Source mold →

Synthesize a Galaxy workflow test plan from a reviewed Workflow Brief, its Galaxy design briefs, and available source evidence.