Build routes, from source to outcome.
Build directly, plan through a reviewable Workflow Brief, or work on an existing Galaxy workflow. Each pipeline composes Molds into one runnable harness.
Run a pipeline → — how to run one end-to-end today.
- Total
- 13
- Phases
- 106
Scroll horizontally to compare every column.
| Pipeline | Journey | Summary | Phases | Status |
|---|---|---|---|---|
| CWL → GALAXY | Direct Build | Translate a CWL Workflow into a Galaxy gxformat2 workflow, then assemble and run a Galaxy workflow test. | 12 | draft |
| GALAXY WORKFLOW MATURATION | Existing Galaxy workflow | Apply the pinned IWC publication checklist to an existing Galaxy workflow, then validate and retest the matured result. | 4 | draft |
| GALAXY WORKFLOW REVIEW | Existing Galaxy workflow | Post-construction review journey: summarize, validate, and test an existing Galaxy workflow, then apply pinned IWC policy. | 4 | draft |
| INTERVIEW → GALAXY | Direct Build | Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff. | 12 | reviewed |
| INTERVIEW → WORKFLOW BRIEF | Create a Workflow Brief | Summarize an interview source and produce a scoped Workflow Brief for expert review. | 2 | draft |
| NEXTFLOW → CWL | Direct Build | Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set. | 12 | draft |
| NEXTFLOW → GALAXY | Direct Build | Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow. | 13 | reviewed |
| NEXTFLOW → WORKFLOW BRIEF | Create a Workflow Brief | Summarize a Nextflow pipeline and produce a scoped Workflow Brief for expert review. | 2 | draft |
| PAPER → CWL | Direct Build | Direct path from a paper to a CWL Workflow + CommandLineTool set. | 11 | draft |
| PAPER → GALAXY | Direct Build | Direct path from a paper to a Galaxy gxformat2 workflow. No Workflow Brief or CWL intermediate. | 12 | draft |
| PAPER → WORKFLOW BRIEF | Create a Workflow Brief | Summarize a paper source and produce a scoped Workflow Brief for expert review. | 2 | draft |
| UPDATE-INTERVIEW → GALAXY | Existing Galaxy workflow | Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop. | 9 | reviewed |
| WORKFLOW BRIEF → GALAXY | Build from a Workflow Brief | Consume an expert-reviewed, unchanged Workflow Brief directly through the Galaxy design and implementation chain. | 11 | draft |
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-subagentsto isolate phase context and--checkpointto commit the run directory after each phase.
The Usage page groups all 13 runnable harnesses into Direct Build, Plan & Build, and existing Galaxy workflow routes.