Which command should I use?

This page maps common tasks to the stable RAFT commands used throughout the main documentation. If you already saw an error or unexpected result, see Troubleshooting.

Start or run a workflow

Create and run a new off-the-shelf project when you already have a manifest:

$ raft run \
    --project-id my-project \
    --workflow lens \
    --version v1.9-dev \
    --species human \
    --input-data fastqs \
    --manifest my_manifest.tsv

Create the project but stop before launching Nextflow:

$ raft run \
    --project-id my-project \
    --workflow lens \
    --version v1.9-dev \
    --manifest my_manifest.tsv \
    --setup-only

Run or resume an existing project:

$ raft run --project-id my-project

Inspect a project

Start with the read-only status command:

$ raft project-status --project-id my-project

Use JSON when another tool needs to consume the result:

$ raft project-status --project-id my-project --json

Validate or create a manifest

Open the manifest generator by omitting --manifest during new project setup, or use the browser-based manifest generator.

Create a command-line TSV starter:

$ raft manifest-template --output my_manifest.tsv

Validate a manifest:

$ raft check-manifest --manifest my_manifest.tsv

Review outputs

Open or generate report files:

$ raft generate-reports --project-id my-project

If the project status output reports failed Nextflow tasks, inspect:

  • outputs/reports/trace-*.txt

  • logs/.nextflow.log

  • task work directories reported by Nextflow

Discover workflows

List workflow groups:

$ raft available-workflows

Inspect available species/input combinations:

$ raft available-workflows --workflow lens

Inspect one workflow input. By default this prints a compact summary with profiles, steps, default parameter count, and the next command shapes. The setup-only and run command examples omit --manifest because it is optional for new projects; add --manifest <MANIFEST> when you already have one.

$ raft available-workflows --workflow lens --species human --input fastqs

Use --details when you need the full default parameter table:

$ raft available-workflows --workflow lens --species human --input fastqs --details

Use JSON for automation:

$ raft available-workflows --workflow lens --species human --input fastqs --json

The JSON form is compact by default. Add --details when automation needs default parameter values.

Advanced module work

Most users do not need these commands. They are useful when manually assembling or debugging a workflow.

$ raft available-modules
$ raft load-module --project-id my-project --module bwa
$ raft list-steps --project-id my-project --module bwa
$ raft add-step --project-id my-project --module bwa --step bwa_mem

Cluster usage

On a cluster or remote server:

  • run RAFT from the RAFT workspace root, where .raft.cfg exists

  • use raft manifest-template when the browser manifest generator is not convenient

  • use --workflow-profile to avoid launching the config generator

  • use --setup-only to create project files before submitting or reviewing a run