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epigenome-chip-seq.cwl
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epigenome-chip-seq.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
SubworkflowFeatureRequirement: {}
inputs:
fastq1:
type: File
fastq2:
type: File
nthreads:
type: int
default: 4
bowtie2_genome_index:
type: File
secondaryFiles:
- ^.1.bt2
- ^.2.bt2
- ^.3.bt2
- ^.4.bt2
- ^.rev.1.bt2
- ^.rev.2.bt2
samtools_filter_alignments:
type: string
default: "0x4"
samtools_skip_alignments:
type: int
default: 42
macs2_control_bam:
type: File
macs2_organism:
type: string
default: mm
label: "mouse: mm, human: hs"
macs2_p_value:
type: float
default: 0.01
steps:
macs2-fastq1:
run: macs2/macs2.cwl
in:
fastq: fastq1
bowtie2_genome_index: bowtie2_genome_index
samtools_filter_alignments: samtools_filter_alignments
samtools_skip_alignments: samtools_skip_alignments
nthreads: nthreads
macs2_p_value: macs2_p_value
macs2_organism: macs2_organism
macs2_control_bam: macs2_control_bam
out:
- fastqc-result
- fastp-trimmed-fastq
- fastp-html
- bowtie2-sam
- samtools-view-bam
- samtools-index-bam-index
- macs2-model-r
- macs2-peaks-narrow-peak
- macs2-peaks-xls
- macs2-summits-bed
- macs2-treat-pileup-bdg
- macs2-control-lambda-bdg
macs2-fastq2:
run: macs2/macs2.cwl
in:
fastq: fastq2
bowtie2_genome_index: bowtie2_genome_index
samtools_filter_alignments: samtools_filter_alignments
samtools_skip_alignments: samtools_skip_alignments
nthreads: nthreads
macs2_p_value: macs2_p_value
macs2_organism: macs2_organism
macs2_control_bam: macs2_control_bam
out:
- fastqc-result
- fastp-trimmed-fastq
- fastp-html
- bowtie2-sam
- samtools-view-bam
- samtools-index-bam-index
- macs2-model-r
- macs2-peaks-narrow-peak
- macs2-peaks-xls
- macs2-summits-bed
- macs2-treat-pileup-bdg
- macs2-control-lambda-bdg
bedtools-intersect-overlap:
run: ../../tool/bedtools/bedtools_intersect_overlap/bedtools_intersect_overlap.cwl
in:
peaks_narrow_peak_a: macs2-fastq1/macs2-peaks-narrow-peak
peaks_narrow_peak_b: macs2-fastq2/macs2-peaks-narrow-peak
out:
- result-narrow-peak
bedtools-intersect-no-overlap:
run: ../../tool/bedtools/bedtools_intersect_no_overlap/bedtools_intersect_no_overlap.cwl
in:
peaks_narrow_peak_a: macs2-fastq1/macs2-peaks-narrow-peak
peaks_narrow_peak_b: macs2-fastq2/macs2-peaks-narrow-peak
out:
- result-narrow-peak
outputs:
fastqc-result-fastq1:
type: File[]
outputSource: macs2-fastq1/fastqc-result
fastp-trimmed-fastq-fastq1:
type: File
outputSource: macs2-fastq1/fastp-trimmed-fastq
fastp-html-fastq1:
type: File
outputSource: macs2-fastq1/fastp-html
bowtie2-sam-fastq1:
type: File
outputSource: macs2-fastq1/bowtie2-sam
samtools-view-bam-fastq1:
type: File
outputSource: macs2-fastq1/samtools-view-bam
samtools-index-bam-index-fastq1:
type: File
outputSource: macs2-fastq1/samtools-index-bam-index
macs2-model-r-fastq1:
type: File
outputSource: macs2-fastq1/macs2-model-r
macs2-peaks-narrow-peak-fastq1:
type: File
outputSource: macs2-fastq1/macs2-peaks-narrow-peak
macs2-peaks-xls-fastq1:
type: File
outputSource: macs2-fastq1/macs2-peaks-xls
macs2-summits-bed-fastq1:
type: File
outputSource: macs2-fastq1/macs2-summits-bed
macs2-treat-pileup-bdg-fastq1:
type: File
outputSource: macs2-fastq1/macs2-treat-pileup-bdg
macs2-control-lambda-bdg-fastq1:
type: File
outputSource: macs2-fastq1/macs2-control-lambda-bdg
fastqc-result-fastq2:
type: File[]
outputSource: macs2-fastq2/fastqc-result
fastp-trimmed-fastq-fastq2:
type: File
outputSource: macs2-fastq2/fastp-trimmed-fastq
fastp-html-fastq2:
type: File
outputSource: macs2-fastq2/fastp-html
bowtie2-sam-fastq2:
type: File
outputSource: macs2-fastq2/bowtie2-sam
samtools-view-bam-fastq2:
type: File
outputSource: macs2-fastq2/samtools-view-bam
samtools-index-bam-index-fastq2:
type: File
outputSource: macs2-fastq2/samtools-index-bam-index
macs2-model-r-fastq2:
type: File
outputSource: macs2-fastq2/macs2-model-r
macs2-peaks-narrow-peak-fastq2:
type: File
outputSource: macs2-fastq2/macs2-peaks-narrow-peak
macs2-peaks-xls-fastq2:
type: File
outputSource: macs2-fastq2/macs2-peaks-xls
macs2-summits-bed-fastq2:
type: File
outputSource: macs2-fastq2/macs2-summits-bed
macs2-treat-pileup-bdg-fastq2:
type: File
outputSource: macs2-fastq2/macs2-treat-pileup-bdg
macs2-control-lambda-bdg-fastq2:
type: File
outputSource: macs2-fastq2/macs2-control-lambda-bdg
narrow-peak-overlap:
type: File
outputSource: bedtools-intersect-overlap/result-narrow-peak
narrow-peak-no-overlap:
type: File
outputSource: bedtools-intersect-no-overlap/result-narrow-peak