Helpful RAFT options

Most off-the-shelf runs only need a project id, workflow, version, and manifest. The options below are useful when you need more control over how RAFT sets up or runs a project.

Project setup options

Use --setup-only to create the project without launching Nextflow:

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

This writes the RAFT project directory, workflow files, loaded modules, manifest, and parameter configuration, then stops before the Nextflow run. It is useful when you want to inspect or edit the generated project before execution.

--setup-only is not a no-write dry run. RAFT does not currently provide a mode that previews every setup action without creating or editing project files.

Use --skip-downloads with off-the-shelf setup when you want to create the project structure without downloading reference files or demonstration FASTQs:

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

This still initializes the project, fetches workflow configuration, and loads workflow modules. Module loading can take a few minutes.

Use --workflow-profile to apply a prepared workflow configuration instead of launching the config generator:

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

standard means the default profile for that workflow/species/input combination. Some workflows may provide additional profile names.

Use --edit-manifest to open the manifest generator even when you provide an existing manifest:

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

Execution options

Use --profile to pass a Nextflow runtime profile:

$ raft run --project-id my-project --profile slurm

Use --max-mem and --max-cpu to pass workflow-level resource caps:

$ raft run \
    --project-id my-project \
    --max-mem 256.GB \
    --max-cpu 32

These become Nextflow workflow parameters such as --max_mem and --max_cpu.

Use --nf-params to pass additional parameters directly to Nextflow when running an existing project:

$ raft run \
    --project-id my-project \
    --nf-params "--some_param value --another_param TRUE"

Use --no-resume to disable Nextflow resume behavior:

$ raft run --project-id my-project --no-resume

Output and report options

By default, RAFT removes the previous outputs/ directory before running an existing project. Use --keep-previous-outputs to leave existing outputs in place:

$ raft run --project-id my-project --keep-previous-outputs

Use --no-reports to skip Nextflow report, trace, DAG, and timeline generation:

$ raft run --project-id my-project --no-reports

Use --show-all-processes to show unfiltered Nextflow output. Without this option, RAFT hides some noisy status and warning lines:

$ raft run --project-id my-project --show-all-processes

Workflow behavior options

By default, RAFT sets params.clean_intermediates to "TRUE" before running when that parameter exists in the generated workflow. Use --keep-intermediates to leave that parameter unchanged:

$ raft run --project-id my-project --keep-intermediates

Use --include-all-samples to set every params.*include_all_samples assignment in workflow/main.nf to "TRUE" before running:

$ raft run --project-id my-project --include-all-samples

This is workflow-dependent. It only changes parameters that already exist in the generated workflow.

Dataset and cloud options

Use --dataset instead of --manifest when running a supported dataset-prep workflow:

$ raft run \
    --project-id hugolo-demo \
    --workflow lens \
    --version v1.9-dev \
    --dataset HugoLo_IPRES_2016

Use --cloud for advanced CLI cloud runs against bucket-backed paths:

$ raft run \
    --project-id my-project \
    --workflow lens \
    --version v1.9-dev \
    --cloud gs://my-bucket/raft

For most cloud users, the BYOC launcher described in Running RAFT on the cloud is the preferred path.

Global options

Use --verbose or -V for more logging:

$ raft --verbose run --project-id my-project

Use --silent or -q to suppress informational output, including the message of the day:

$ raft --silent run --project-id my-project

Use --bypass-dependencies only for advanced testing or constrained environments where you intentionally want to skip dependency checks:

$ raft --bypass-dependencies run --project-id my-project