Preparing Your Samples

LENS requires a manifest that defines the relationships among your samples, patients, and datasets. The manifest tells RAFT which samples belong together and what sequencing data each sample contains.

The organizational hierarchy follows:

Sample ⊂ Group ⊂ Patient ⊂ Dataset

Samples belong to groups (for multi-timepoint analyses), groups belong to patients, and patients belong to datasets.

_images/patient_names_and_runs.png

A LENS manifest requires at least one tumor DNA sample, one normal DNA sample, and one tumor RNA sample per patient. A reduced analysis (without SNV or InDel pMHCs) can be run with only tumor RNA.

Using the Manifest Generator

The easiest way to create a manifest is through the RAFT Manifest Generator — a browser-based form with autocomplete, real-time validation, and workflow-aware requirements.

Launch it by starting a new project without a --manifest argument:

raft run --project-id my-project-lens --workflow lens --version 1.9-dev

The Manifest Generator opens in your browser. From there you can:

  1. Select a workflow — choose “LENS (Tumor Antigens)” from the dropdown.

  2. Add samples — fill in Dataset, Patient Name, Sample Type, Run Name, and File Prefix for each sample.

  3. Review — the Sample Overview section organizes samples by patient and group, with color-coded type badges.

  4. Save — click “Save to RAFT” to save the manifest to your project.

screenshots/manifest_generator_overview.png

The Sample Type dropdown auto-sets the Run Name prefix and Sequencing Method:

  • Tumor DNA → prefix ad-, method WES

  • Normal DNA → prefix nd-, method WES

  • Tumor RNA → prefix ar-, method RNA-Seq

  • Normal RNA → prefix nr-, method RNA-Seq

The File Prefix field autocompletes from available FASTQ files in your project directory and validates that the files exist.

Validation warnings appear in real time — for example, “Missing for LENS: Normal DNA” if a normal DNA sample has not been added for a patient.

screenshots/manifest_generator_validation.png

A hosted version of the Manifest Generator is also available for creating manifests outside of a project:

Creating a manifest from the command line

If you prefer the command line, RAFT can generate a starter manifest:

raft manifest-template --output my_manifest.tsv

This creates a TSV file with example rows for a typical LENS run. To generate a header-only template:

raft manifest-template --no-examples --output my_manifest.tsv

For the full column reference, sample naming conventions, complex sample sets with Groups, and manifest validation, see Manifest Specifications.

Supplying the manifest

Once you have a manifest, pass it when starting a project:

raft run --project-id my-project-lens --workflow lens --version 1.9-dev --manifest my_manifest.tsv

Manifest files must be placed in RAFT’s inputs/metadata directory to be discovered automatically.