CWL Workflow: wf_split_self_and_idr.cwl

Workflow: wf_split_self_and_idr.cwl

Fetched 2026-01-16 02:13:03 GMT

Verified with cwltool version 3.1.20221201130942

This workflow returns the reproducible number of split peaks given a single bam file and its size-matched input pair. This workflow splits the bam file first, but does not do anything to the input.

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Inputs/Outputs

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Inputs

ID	Type	Title	Doc
species	String
clip_bam	File
input_bam	File
chrom_sizes	File
merged_peaks_bed	String
merged_peaks_custombed	String

Steps

ID	Runs	Doc
index_split1	samtools-index.cwl (CommandLineTool)	samtools-index.cwl is developed for CWL consortium
index_split2	samtools-index.cwl (CommandLineTool)	samtools-index.cwl is developed for CWL consortium
step_bam_split	bam_split.cwl (CommandLineTool)	Runs a wrapper script that randomly splits a BAM file, without replacement.
step_clipper_split1	clipper.cwl (CommandLineTool)	CLIPper is a tool to define peaks in your CLIP-seq dataset. CLIPper was developed in the Yeo Lab at the University of California, San Diego. Usage: clipper --bam CLIP-seq_reads.srt.bam --species hg19 --outfile CLIP-seq_reads.srt.peaks.bed
step_clipper_split2	clipper.cwl (CommandLineTool)	CLIPper is a tool to define peaks in your CLIP-seq dataset. CLIPper was developed in the Yeo Lab at the University of California, San Diego. Usage: clipper --bam CLIP-seq_reads.srt.bam --species hg19 --outfile CLIP-seq_reads.srt.peaks.bed
step_reproducible_peaks_num	wf_get_reproducible_eclip_peaks.cwl (Workflow)	The main workflow that produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each).

Outputs

ID	Type	Label	Doc
rep1_clip_read_num	File
rep2_clip_read_num	File
rep1_input_read_num	File
rep2_input_read_num	File
merged_peaks_bed_file	File
reproducing_peaks_count	Integer