Nextflow Parameters

All parameters for the Krewlyzer Nextflow pipeline.

Required Parameters

Parameter	Description
--samplesheet	CSV with sample information
--ref	Reference genome FASTA

General Parameters

Parameter	Default	Description
--outdir	./results	Output directory
--asset_dir		Base directory for PON/targets (enables assay resolution)
--targets		Global target BED (fallback)
--genome	hg19	Genome build (hg19 or hg38)
--threads	8	Threads per process
--verbose	false	Enable verbose logging

PON Parameters

Parameter	Default	Description
--pon_model		Global PON model (fallback)
--pon_variant	all_unique	PON variant: all_unique or duplex
--skip_pon	false	Skip PON z-score normalization

Feature Parameters

Parameter	Default	Description
--bait_padding	50	Bait edge padding for WPS
--maxlen	1000	Maximum fragment length
--no_tfbs	false	Disable TFBS region entropy
--no_atac	false	Disable ATAC region entropy

See Also

• Samplesheet Format
• CLI Parameters