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Nextflow Pipeline

Run gbcms at scale on HPC clusters with automatic parallelization.

Overview

The Nextflow workflow provides:

  • DNA and RNA modes with dedicated modules
  • Automatic parallelization across samples
  • SLURM/HPC integration with resource management
  • Containerization with Docker/Singularity
  • Resume capability for failed runs

Pipeline Architecture

flowchart TD
    CSV(["📄 samplesheet.csv"]):::input --> Parse[Parse Samplesheet]
    MAF(["📄 variants.maf"]):::input --> FilterCheck{"filter_by_sample
AND .maf input?"}
    Parse --> FilterCheck

    FilterCheck -->|Yes| FilterMAF["FILTER_MAF
(per-sample MAF extraction)"]
    FilterCheck -->|No| Ready[All samples get full variants file]

    FilterMAF --> HasData{Variants found?}
    HasData -->|Yes| Ready2[Join filtered MAF with BAM]
    HasData -->|No| Skip(["⚪ Skip sample"]):::skip
    FilterMAF --> Summary["PIPELINE_SUMMARY
(aggregate filter stats)"]

    Ready --> ModeCheck{mode?}
    Ready2 --> ModeCheck

    ModeCheck -->|dna| DNA["GBCMS_DNA
(cfDNA/somatic counting)"]:::dna
    ModeCheck -->|rna| RNA["GBCMS_RNA
(RNA-seq counting)"]:::rna

    DNA --> DNAOut(["📊 DNA VCF/MAF"]):::output
    RNA --> RNAOut(["📊 RNA VCF/MAF"]):::output
    Summary --> SummaryOut(["📋 pipeline_summary.tsv"]):::output

    classDef input fill:#3498db,color:#fff,stroke:#2471a3,stroke-width:2px;
    classDef dna fill:#27ae60,color:#fff,stroke:#1e8449,stroke-width:2px;
    classDef rna fill:#e74c3c,color:#fff,stroke:#c0392b,stroke-width:2px;
    classDef output fill:#9b59b6,color:#fff,stroke:#7d3c98,stroke-width:2px;
    classDef skip fill:#95a5a6,color:#fff,stroke:#7f8c8d,stroke-width:2px;
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Quick Start

# DNA mode (default)
nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    -profile docker

# RNA mode
nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.maf \
    --fasta reference.fa \
    --mode rna \
    -profile docker

Documentation

Page Description
Samplesheet Input CSV format
Parameters All configuration options
Examples Common usage patterns