Foundry
Harness Pipelines

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
79
PipelineSummaryPhasesStatus
CWL → GALAXY Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction. 11 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. 12 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.

  1. Install the harness skills. They install like any Foundry cast skill — via the Claude Code plugin marketplace or copied into ~/.claude/skills/. See Install.
  2. 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.
  3. 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.
  4. Optional run flags. Pass --use-subagents to run each cast phase in its own subagent (one per loop iteration) so the orchestrator's context stays small, and --checkpoint to git init the 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.