Accessing and Reviewing Outputs

The recommended way to review LENS outputs is through the RAFT Output Viewer — an interactive web interface for exploring pMHC reports, QC metrics, and cohort comparisons.

Launching the viewer

After a LENS run completes:

raft generate-reports --project-id my-project-lens

A demonstration report is also available:

raft generate-reports --demo

Navigating the viewer

The viewer provides several views, accessible from the sidebar:

Report view

The primary view for exploring predicted pMHCs:

Select a patient from the sidebar to load their report
Each pMHC is displayed as a card showing peptide sequence, HLA allele, antigen source badge (color-coded by type), and key metrics
Filter by Top N, sort metric, allele, or antigen source
Interactive visualizations (histograms, scatter plots, box plots) appear alongside the cards

QC view

Sample-level quality control metrics organized by sample type:

Tumor DNA — alignment stats, coverage, variant calling metrics
Tumor RNA — alignment stats, RNA quality, expression metrics
Normal DNA — alignment stats, somalier relatedness checks
HLA typing — allele calls with confidence scores
Germline phasing — WhatsHap phasing summary

Cohort QC view

Cross-patient QC metrics in a table format for comparing samples across the entire project.

Joint Analysis view

For patients with multiple groups (e.g., pre- and post-treatment):

pMHC sharedness — Venn diagram showing shared vs. exclusive pMHCs
Expression changes — gene expression comparison across groups
Gained/lost antigens — antigens unique to each group
Allelic consistency — HLA allele consistency checks

For a guide to interpreting the report columns and prioritization scores, see Interpreting the Report. For exhaustive column-by-column documentation, see Report Column Reference.

Output directory structure

RAFT saves all outputs under the project’s outputs/ directory:

``outputs/samples/`` — sample-level outputs (BAMs, VCFs, quantifications, etc.)
``outputs/qc/`` — quality control summaries and metrics
``outputs/reports/`` — Nextflow execution reports, traces, and timelines
``outputs/lens/`` — the primary LENS report (*.report.tsv) and run QC summary (*.run_qc_summary.tsv)

Directory names map directly to manifest fields: Dataset/, Patient_Name/, and Run_Name/. Combined run directories (e.g., ad-123+nd-234/) represent outputs from paired or grouped inputs.

To find specific file types:

# VCF files
find outputs/ -name "*vcf*"
# BAM files
find outputs/ -name "*.bam"
# LENS reports
find outputs/ -name "*.report.tsv"