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Nextflow Parameters

All parameters for the Krewlyzer Nextflow pipeline. See nextflow.config for defaults.

Required Parameters

Parameter Description
--samplesheet CSV with sample information (format)
--ref Reference genome FASTA (indexed)

General Parameters

Parameter Default Description
--outdir ./results Output directory
--asset_dir Base directory for PON/targets (enables assay resolution)
--targets Global target BED (fallback if not in samplesheet)
--genome hg19 Genome build (hg19 or hg38)
--threads 8 Threads per process
--verbose false Enable verbose logging

Mode Selection

Parameter Default Description
--use_runall true true = unified run-all (default), false = tool-level subworkflow

PON Parameters

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

Panel & WPS Parameters

Parameter Default Description
--bait_padding 50 Bait edge padding for WPS (bp)
--wps_anchors Custom WPS anchors BED (auto-loaded from assay if not set)
--wps_background Custom WPS background Alu BED (auto-loaded if not set)

Filter & Algorithm Parameters

Parameter Default Description
--mapq 20 Minimum mapping quality
--minlen 65 Minimum fragment length
--maxlen 1000 Maximum fragment length
--min_baseq 20 Minimum base quality for mFSD variant calling
--duplex true Enable duplex weighting for mFSD (graceful fallback)
--skip_duplicates true Skip duplicate reads
--require_proper_pair false Require proper pairs (disable for duplex BAMs)
--exclude_regions BED file of regions to exclude

Feature Toggles

Parameter Default Description
--no_tfbs false Disable TFBS region entropy
--no_atac false Disable ATAC region entropy
--skip_target_regions false Force WGS mode (ignore bundled targets)
--disable_e1_aggregation false Skip E1-only FSC aggregation
--region_mds_e1_only false Run region-MDS on E1 (first exon) only

Output Parameters

Parameter Default Description
--generate_json true Generate unified features.json for ML pipelines
--output_format tsv Feature output format: tsv, parquet, or both. WPS outputs are always Parquet regardless of this setting.
--compress_tsv false Gzip-compress all TSV outputs (.tsv.gz). Applies only when output_format is tsv or both. Maps to the --compress flag in the Python CLI.

See Also