Getting Started

This page gives the fastest path to use the UX wrapper safely.

Quick start

  1. Create starter config:

pleb init

  1. Apply a preset:

pleb profile list
pleb profile use minimal --config configs/runs/pipeline/pleb.pipeline.toml

  1. Inspect resolved mapping:

pleb doctor --config configs/runs/pipeline/pleb.pipeline.toml
pleb explain --config configs/runs/pipeline/pleb.pipeline.toml

  1. Run:

pleb run --config configs/runs/pipeline/pleb.pipeline.toml

Golden-path journey shortcuts:

pleb run detect --config configs/runs/pipeline/pleb.pipeline.toml --confirm
pleb run apply --config configs/runs/pipeline/pleb.pipeline.toml --confirm
pleb run publish --config configs/runs/pipeline/pleb.pipeline.toml

Plan first (no execution):

pleb run --config configs/runs/pipeline/pleb.pipeline.toml --plan

  1. Override a setting without editing file:

pleb run --config configs/runs/pipeline/pleb.pipeline.toml --set data.jobs=8 --set run.run_pqc=true

Command reference

pleb init

Creates starter UX config files.

pleb init --config pleb.toml --force

Mode-specific starter (with verbosity):

pleb init --mode pipeline --level minimal
pleb init --mode pipeline --level balanced
pleb init --mode pipeline --level full
pleb init --mode ingest
pleb init --mode workflow
pleb init --mode qc-report

Generate one file per mode:

pleb init --all-modes --outdir configs --level balanced --force

Generate a 3-pass workflow blueprint (detect -> apply -> post-clean):

pleb init --workflow-template 3pass-clean --outdir configs --force

Use --force only when you explicitly want to overwrite.

pleb profile list

Lists preset names from configs/presets/*.toml.

pleb profile use <name>

Deep-merges a preset into your UX config.

pleb profile use balanced --config pleb.toml

pleb doctor

Runs lightweight validation and prints a quick summary of resolved mode and required keys.

pleb explain

Prints section-level UX->legacy mapping summary for debugging.

pleb run

Translates UX config into the current flat PLEB config and routes to the selected mode execution.

Profiles can be applied at run time before --set overrides:

pleb run --config configs/runs/pipeline/pleb.pipeline.toml --profile balanced

What files you edit vs what you do not edit

Edit directly:

  • pleb.toml

Usually do not edit directly (unless advanced use):

  • configs/runs/*

  • configs/workflows/*

  • configs/catalogs/*

  • configs/rules/*

Common first-run checklist

  • Set paths.home_dir correctly.

  • Set paths.singularity_image correctly.

  • Set desired branch scope under data.

  • Confirm run.mode (pipeline/ingest/workflow/qc-report).

  • Use doctor before first run.