Nextflow Outputs

Output files produced by the Nextflow pipeline.

Output Directory Structure

results/
├── extract/
│   ├── {sample}.bed.gz
│   └── {sample}.bed.gz.tbi
├── motif/
│   ├── {sample}.EndMotif.tsv
│   └── {sample}.MDS.tsv
├── fsc/
│   ├── {sample}.FSC.tsv
│   └── {sample}.FSC.gene.tsv
├── fsd/
│   └── {sample}.FSD.tsv
├── fsr/
│   └── {sample}.FSR.tsv
├── wps/
│   ├── {sample}.WPS.parquet
│   └── {sample}.WPS_background.parquet
├── ocf/
│   └── {sample}.OCF.tsv
├── region_entropy/
│   ├── {sample}.TFBS.tsv
│   └── {sample}.ATAC.tsv
├── region_mds/
│   ├── {sample}.MDS.exon.tsv
│   └── {sample}.MDS.gene.tsv
├── mfsd/
│   └── {sample}.mFSD.tsv
└── uxm/
    └── {sample}.UXM.tsv

Panel Mode Outputs

When --targets is provided, outputs are split:

File	Content
{sample}.FSC.tsv	Off-target features
{sample}.FSC.ontarget.tsv	On-target features

Available Modules

Module	Description
KREWLYZER_EXTRACT	Fragment extraction
KREWLYZER_FSC	Fragment Size Coverage
KREWLYZER_FSR	Fragment Size Ratio
KREWLYZER_FSD	Fragment Size Distribution
KREWLYZER_WPS	Windowed Protection Score
KREWLYZER_OCF	Orientation cfDNA Fragmentation
KREWLYZER_MOTIF	End Motif & MDS
KREWLYZER_REGION_ENTROPY	TFBS/ATAC entropy
KREWLYZER_REGION_MDS	Per-gene MDS
KREWLYZER_UXM	Methylation
KREWLYZER_MFSD	Mutant Fragment Size
KREWLYZER_RUNALL	Full pipeline
KREWLYZER_BUILD_PON	Build PON