Preparing your samples

RAFT supports both user-provided samples and off-the-shelf immuno-oncology datasets.

Making your files available to RAFT

RAFT starts each workflow using sample-associated data. These data could be FASTQs, BAMs, VCFs, or RNA count data. Regardless of the type of input data, they all need to be made discoverable by RAFT. Users can make input files discoverable by RAFT by copying or symlinking them into the RAFT inputs/ directories, for example /path/to/raft/inputs/fastqs. Grouping input files by dataset, such as /path/to/raft/inputs/fastqs/my_favorite_dataset/samp1_1.fq.gz, is recommended but not required.

Note

Input data for demonstration workflows and off-the-shelf datasets are downloaded automatically.

The RAFT manifest

A manifest describes the samples in a dataset and tells RAFT:

how the samples should be named
how the samples are related
what input files are associated with each sample

For user-provided datasets, you supply this manifest directly. For supported off-the-shelf datasets, RAFT can generate the run manifest automatically as part of dataset preparation.

Using an off-the-shelf dataset

The table below lists the currently supported off-the-shelf immuno-oncology datasets. Click a dataset name to view its publication, abstract, and README.

Loading datasets from GitLab...

Specifying an off-the-shelf dataset with RAFT

To create a new project from an off-the-shelf dataset, simply pass --dataset and the dataset’s identifier to RAFT:

$ raft run \
    --project-id my-project \
    --workflow lens \
    --dataset <DATASET_NAME> \
    --version v1.9-dev \

RAFT will clone the dataset-prep module, download the required FASTQs from ENA/EBI, and stage them before execution. No user-provided manifest is required; the run manifest is generated automatically.

Using your own samples

Running your own samples through RAFT requires creating a manifest for your dataset. RAFT provides a web-based interface to help generate that manifest. This interface becomes available when you execute raft run on a new project for the first time.

If you prefer to create the manifest separately and then provide it with raft run ... --manifest <MANIFEST_FILE_NAME.tsv>, you can use the hosted manifest generator here.

More information about the manifest format is available in Manifest Specifications.

Specifying your own samples with RAFT

If you already have a manifest, create a new project by passing --manifest and the manifest filename.

Note

Manifest TSVs must be in your RAFT’s inputs/metadata directory to be discovered by RAFT.

$ raft run \
    --project-id my-project \
    --workflow lens \
    --version v1.9-dev \
    --manifest <MANIFEST_NAME.TSV>

Alternatively, if you want to make your manifest as part of running RAFT, then simply run RAFT without --manifest:

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