Nextflow Parameters

Complete reference for all pipeline parameters.

Required Parameters

Parameter	Description
--input	Path to samplesheet CSV
--variants	Path to VCF/MAF variants file
--fasta	Reference FASTA (with .fai index)

Output Options

Parameter	Default	Description
--outdir	results	Output directory
--format	vcf	Output format (vcf or maf)
--suffix	''	Suffix for output filenames

Filtering Options

Parameter	Default	Description
--min_mapq	20	Minimum MAPQ
--min_baseq	0	Minimum BASEQ
--filter_duplicates	true	Filter duplicate reads
--filter_secondary	false	Filter secondary alignments
--filter_supplementary	false	Filter supplementary alignments
--filter_qc_failed	false	Filter QC failed reads
--filter_improper_pair	false	Filter improperly paired reads
--filter_indel	false	Filter reads with indels

Resource Limits

Parameter	Default	Description
--max_cpus	16	Maximum CPUs per job
--max_memory	128.GB	Maximum memory per job
--max_time	240.h	Maximum runtime per job

Performance Benchmarks

Representative metrics from cfDNA duplex BAM samples:

Sample Type	BAM Size	Variants	Runtime	CPUs
ctDNA (plasma)	1.3 GB	608	~25s	4
Plasma control	776 MB	608	~20s	4

Execution Profiles

Profile	Description
docker	Local with Docker containers
singularity	HPC with Singularity
slurm	SLURM cluster with Singularity
local	No container (requires local install)

Related

• Samplesheet — Input format

• Examples — Usage patterns

• CLI Reference — Underlying command