Workflow: wf_split_self_and_idr.cwl

Fetched 2023-01-10 07:08:17 GMT

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

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 Label 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

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
Permalink: https://w3id.org/cwl/view/git/aedc0a14d4ba109ee65678a3201a52c5bb6ad473/cwl/wf_split_self_and_idr.cwl