CWL Workflow: wf_self_consistency_ratio.cwl

Workflow: wf_self_consistency_ratio.cwl

Fetched 2023-01-14 21:36:36 GMT

Verified with cwltool version 3.1.20221201130942

Computes the self-consistency ratio (see Gabe's protocols paper, or CHIP SEQ). Given two replicates, split each and perform IDR on each fragment. Returns the ratio of max(N1, N2)/min(N1, N2) where N1, N2 are the numbers of reproducible peaks found between each rep split pair.

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Inputs/Outputs

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Inputs

ID	Type	Title	Doc
species	String
rep1_name	String
rep2_name	String
rep1_clip_bam_file	File
rep2_clip_bam_file	File
rep1_input_bam_file	File
rep2_input_bam_file	File
rep1_merged_peaks_bed	String
rep2_merged_peaks_bed	String
rep1_merged_peaks_custombed	String
rep2_merged_peaks_custombed	String

Steps

ID	Runs	Doc
step_self_consistency	max_over_min.cwl (CommandLineTool)
step_split_rep1_and_idr	wf_split_self_and_idr.cwl (Workflow)	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.
step_split_rep2_and_idr	wf_split_self_and_idr.cwl (Workflow)	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.

Outputs

ID	Type	Label	Doc
self_consistency_ratio	File
rep1_reproducing_peaks_count	Integer
rep2_reproducing_peaks_count	Integer