Nextflow Parameters

Complete reference for all pipeline parameters.

Required Parameters

Parameter
Description

--input

--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)

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