Ordered Mold sequences.
Pipelines compose Molds into harness journeys and make the Foundry navigable from source to target.
Run a pipeline → — how to run one end-to-end today.
- Total
- 7
- Phases
- 81
| Pipeline | Summary | Phases | Status |
|---|---|---|---|
| CWL → GALAXY | Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction. | 12 | draft |
| INTERVIEW → GALAXY | Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff. | 12 | draft |
| NEXTFLOW → CWL | Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set. | 12 | draft |
| NEXTFLOW → GALAXY | Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow. | 13 | draft |
| PAPER → CWL | Direct path from a paper to a CWL Workflow + CommandLineTool set. | 11 | draft |
| PAPER → GALAXY | Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate. | 12 | draft |
| 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 | draft |
Run a pipeline
/ how to run one end-to-end today
A Foundry pipeline is an ordered sequence of Molds that walks a source workflow to a target
workflow. You run one today via its assembled pipeline-* harness
skill — a stop-gap that invokes each phase's cast in order.
- Install the harness skills. They install like any Foundry cast skill through the Claude Code or Codex plugin metadata around the same shared bundle. See Install.
- Make the runtime available. Pipelines call out to
gxwf(schema/validation), Planemo (test execution), and the Foundry validators. Install these in the environment before a run that reaches the validate/test phases. - Invoke the harness for the pipeline you want. Each run gets its own
./<run-slug>/working directory, so artifacts stay namespaced and a second run won't clobber the first — the harness creates it before phase 1. - Optional run flags. Pass
--use-subagentsto run each cast phase in its own subagent (one per loop iteration) so the orchestrator's context stays small, and--checkpointtogit initthe run directory and commit after every phase — a per-step history for workflow-implementation visualizations. Both default off and compose.
See the 7 runnable harnesses on Usage → — invoke command, phase counts, and install steps.