Frequently asked questions

This page collects common RAFT questions about setup, manifests, projects, and workflow execution. If you are diagnosing a failure or unexpected behavior, start with Troubleshooting.

What is RAFT?

RAFT (Reproducible Analyses Framework and Tools) is a workflow manager for building, running, packaging, and reviewing bioinformatics projects in a consistent way. It helps organize inputs, references, workflow code, logs, and outputs under a reproducible project structure.

What directory should I run RAFT from?

Run workspace-level RAFT commands from the workspace root, the directory that contains .raft.cfg.

If you are unsure where that is, check the path you used for:

$ raft setup --default

If a command says RAFT cannot find .raft.cfg, change back to the workspace root and rerun it there.

Do I need a manifest before I create a project?

Not always. For many workflow runs, --manifest is optional during initial setup. If you omit it, RAFT can open the manifest generator so you can create one interactively.

For example:

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

If you prefer command-line creation, generate a starter TSV with:

$ raft manifest-template --output my_manifest.tsv

What does `--setup-only` do?

--setup-only prepares the project but does not launch Nextflow. Depending on the workflow, it may:

create the project directory structure
fetch workflow configuration and modules
load metadata and references
generate or save manifest/config files

Use it when you want to inspect or edit the generated project before running:

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

How do I rerun an existing project?

Use the project ID:

$ raft run --project-id my-project

If the project has already run before, RAFT and Nextflow will attempt to resume work unless you disable resume behavior explicitly.

How do I see what happened in a project?

Start with the project summary:

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

That is the safest first command for inspection because it is read-only and surfaces workflow context, manifest details, trace/report locations, and next steps.

Where are my workflow outputs?

RAFT projects usually store outputs under:

projects/<PROJECT_ID>/outputs/
projects/<PROJECT_ID>/outputs/reports/ for Nextflow reports and traces
projects/<PROJECT_ID>/logs/ for execution logs

The exact workflow-specific files depend on the workflow you ran. See Accessing and reviewing outputs for the general layout.

Can I run RAFT without a default Nextflow profile?

Yes, but only with caveats. RAFT can continue with conservative local resource caps when it does not detect a standard/default profile in ~/.nextflow/config.

For a real cluster or production run, pass a profile explicitly:

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

How do I update references for an off-the-shelf workflow?

For OTS workflows, use:

$ raft download-refs --workflow lens --version v1.9-dev --species human

This populates the shared references area for that workflow. If you are using a bucket-backed run with --references-bucket, make sure the required staged reference outputs are also present in that bucket before launching the run.

How do I open the report viewer?

For an existing project:

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

You can also launch the viewer without preloading project files:

$ raft generate-reports --project-id my-project --no-load