Workflow: chipseq_tf.cwl

Fetched 2022-08-08 20:24:56 GMT
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Inputs

ID Type Title Doc
idxbase File

Base filename of bwa index to map against

blacklist File

Blacklist regions to remove

replicates https://w3id.org/cwl/view/git/f6346c109000c92ae53183df844eece0ad63eeb7/replicatesa87006fc-8f65-4199-9851-f54e186e0cab[]

List of replicates

Steps

ID Runs Label Doc
idr
tools/idr.cwl (CommandLineTool)
name_outputs
chipseq_tf.cwl#name_outputs/c590eb13-33d0-4052-ba4a-2971c71e26ef (ExpressionTool)
align_control
align_treatment
pooled_call_peaks
tools/macs-callpeak.cwl (CommandLineTool)
replicate_call_peaks
tools/macs-callpeak.cwl (CommandLineTool)
pooled_replicates_control
tools/samtools-merge.cwl (CommandLineTool)
pooled_replicates_treatment
tools/samtools-merge.cwl (CommandLineTool)

Outputs

ID Type Label Doc
idr_narrowpeak_file File

Peaks surviving IDR using pooled peaks as oracle

pooled_narrowpeak_file File

Peaks for each replicate

replicate_narrowpeak_files File[]

Peaks from pooling replicates

Permalink: https://w3id.org/cwl/view/git/f6346c109000c92ae53183df844eece0ad63eeb7/chipseq_tf.cwl