Workflows vs Templates

Pick the right abstraction for your job: single tool (template) or orchestration (workflow).

Templates

Descriptor: templates/<id>/template_config.yaml.
Capabilities: params, render files, run entry, hooks, publish.
State: params and published values persist in project.yaml.
CLI: bpm template render/run/publish <id>.

Workflows

Descriptor: workflows/<id>/workflow_config.yaml (similar shape to templates for params/run).
Capabilities: params, run entry, hooks; no built‑in publish.
State: can record run history in project.yaml when --project is provided.
CLI: bpm workflow run <id>.

Defaults and paths

bpm workflow run executes in the workflow folder; entry defaults to run.sh if not set.

Minimal workflow example

# workflows/clean/workflow_config.yaml
id: clean
description: Remove intermediates
params:
  keep_logs: {type: bool, default: true}
run:
  entry: run.sh

When to choose

Use templates for atomic, publishable units (e.g., “demux”, “align”, “multiqc”).
Use workflows to wrap multiple steps or to add orchestration without introducing a new engine.