🧬CCRGeneticsBranch / Oncogenomics_NF_WF

The Oncogenomics_NF_WF is a containerized Nextflow pipeline for processing exome and RNA-seq cancer data. It is built for scalable execution on HPC (Biowulf) and AWS. It integrates tools for variant calling, CNV detection, mutational signatures, TMB, HLA typing, neoantigen prediction, RNA quantification, fusion detection, and immune infiltration metrics. It currently supports hg19 and mm39 reference genomes. Efforts ongoing to expand support for hg38. For GRCm39 (mm39) reference, only mapping and RSEM quantification is supported.

Requirements

• Nextflow (>= 23.10.0)
• Graphviz 2.40
• Docker or Singularity 3.10.5
• Access to Biowulf HPC or AWS Batch

Usage

# Run on Biowulf

/data/khanlab/projects/Nextflow_dev/dev/vg_dev/Oncogenomics_NF_WF/launch.py --help

usage: launch.py [-h] (--samplesheet SAMPLESHEET | --patient PATIENT) [--casename CASENAME] [--inputdir INPUTDIR] [--outdir OUTDIR] [--genome {hg19,mm39}]
                 [--platform PLATFORM] [--profile PROFILE] [--no-resume] [--no-cleanup]

Submit the Oncogenomics Nextflow workflow to SLURM.

optional arguments:
  -h, --help            show this help message and exit
  --samplesheet SAMPLESHEET
                        Path to existing samplesheet CSV
  --patient PATIENT     Patient ID (requires --casename to build a samplesheet)
  --casename CASENAME   Case name (required with --patient)
  --inputdir INPUTDIR   Optional input directory passed to samplesheet_builder.py
  --outdir OUTDIR       Results root directory (default: /data/khanlab/projects/processed_DATA)
  --genome {hg19,mm39}  Genome (default: hg19)
  --platform PLATFORM   Platform label (default: biowulf)
  --profile PROFILE     Explicit Nextflow profile (overrides genome→profile mapping)
  --no-resume           Run Nextflow without -resume
  --no-cleanup          Disable cleanup (default: cleanup runs after successful job)

Input / Output

Input: Sample sheet with paths to fastq or bam/cram files. Link to samplesheet guidelines.

Output: VCFs, CNV calls, mutational signatures, TMB metrics, HLA predictions, neoantigen candidates, expression matrices, fusion calls, immune infiltration metrics, QC reports.

Results are organized by patientID/casename with an option to visualize data at clinOmics data portal

Documentation

Full documentation is available here: 👉 Oncogenomics_NF_WF Documentation

Contributing

Issues and pull requests are welcome. Please follow coding and documentation guidelines.

Please send your comments/questions/suggestions to Vineela Gangalapudi via email.