CWL Workflow: ChIP-Seq

Workflow: ChIP-Seq

Fetched 2026-10-11 10:48:48 GMT

Verified with cwltool version 3.1.20230201224320

This workflow execute peak caller and QC from ChIP-Seq. For TF 1. Do not use broad, call-summits, broad-cutoff. 2. nomodel = True For Histones (H3K27me3, H3K9me3, H3K36me3): 1. Use broad, call-summits, broad-cutoff == 0.1. 2. nomodel = False For other histone marks: 1. Do not use broad, broad-cutoff. 2. nomodel = False 3. call-summits = True

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Default Values
Nested Workflows
Tools
Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/master/LICENSE

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
broad	Boolean (Optional)
extsize	Integer (Optional)
nomodel	Boolean (Optional)
input_bam	File
control_bam	File (Optional)
bam_flagstat	File
broad-cutoff	Float (Optional)
call-summits	Boolean (Optional)
cutoff-analysis	Boolean (Optional)
macs_callpeaks_g	String
macs_callpeaks_q	Float

Steps

ID	Runs	Label	Doc
macs_cutoff	../../tools/R/macs-cutoff.cwl (CommandLineTool)	MACS2_cutoff	Inflection point calculated from MACS2 peaks file
macs_callpeak	../../tools/macs/macs3-callpeak.cwl (CommandLineTool)	MACS3-callpeak	BASH echo command
macs_callpeak_q_value	../../tools/macs/macs3-callpeak.cwl (CommandLineTool)	MACS3-callpeak	BASH echo command

Outputs

ID	Type	Label	Doc
bed	File (Optional)
xls	File
lambda	File
pileup	File
broadPeak	File (Optional)
gappedPeak	File (Optional)
narrowPeak	File (Optional)
macs_cutoff_pdf	File (Optional)
macs_cutoff_inflection	File (Optional)