CWL Workflow: epigenome-chip-seq.packed.cwl#main

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

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

Inputs

ID	Type	Title
fastq1	File
fastq2	File
nthreads	Integer
macs2_p_value	Float
macs2_organism	String	mouse: mm, human: hs
macs2_control_bam	File
bowtie2_genome_index	File
samtools_skip_alignments	Integer
samtools_filter_alignments	String

ID	Runs	Doc
macs2-fastq1	epigenome-chip-seq.packed.cwl#macs2.cwl (Workflow)
macs2-fastq2	epigenome-chip-seq.packed.cwl#macs2.cwl (Workflow)
bedtools-intersect-overlap	epigenome-chip-seq.packed.cwl#bedtools_intersect_overlap.cwl (CommandLineTool)	bedtools intersect allows one to screen for overlaps between two sets of genomic features.
bedtools-intersect-no-overlap	epigenome-chip-seq.packed.cwl#bedtools_intersect_no_overlap.cwl (CommandLineTool)	bedtools intersect allows one to screen for overlaps between two sets of genomic features.

ID	Type	Label	Doc
fastp-html-fastq1	File
fastp-html-fastq2	File
bowtie2-sam-fastq1	File
bowtie2-sam-fastq2	File
narrow-peak-overlap	File
fastqc-result-fastq1	File[]
fastqc-result-fastq2	File[]
macs2-model-r-fastq1	File
macs2-model-r-fastq2	File
macs2-peaks-xls-fastq1	File
macs2-peaks-xls-fastq2	File
narrow-peak-no-overlap	File
macs2-summits-bed-fastq1	File
macs2-summits-bed-fastq2	File
samtools-view-bam-fastq1	File
samtools-view-bam-fastq2	File
fastp-trimmed-fastq-fastq1	File
fastp-trimmed-fastq-fastq2	File
macs2-treat-pileup-bdg-fastq1	File
macs2-treat-pileup-bdg-fastq2	File
macs2-peaks-narrow-peak-fastq1	File
macs2-peaks-narrow-peak-fastq2	File
macs2-control-lambda-bdg-fastq1	File
macs2-control-lambda-bdg-fastq2	File
samtools-index-bam-index-fastq1	File
samtools-index-bam-index-fastq2	File