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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
doc: 'ChIP-seq - Quantification - samples: treatment and control'
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
input_trt_bam_files:
type: File[]
input_ctrl_bam_files:
type: File[]
input_genome_sizes:
type: File
nthreads:
default: 1
type: int
steps:
bedtools_genomecov:
run: ../map/bedtools-genomecov.cwl
scatter: ibam
in:
bg:
valueFrom: ${return true}
g: input_genome_sizes
ibam: input_trt_bam_files
out:
- output_bedfile
bedsort_genomecov:
run: ../quant/bedSort.cwl
scatter: bed_file
in:
bed_file: bedtools_genomecov/output_bedfile
out:
- bed_file_sorted
bdg2bw-raw:
run: ../quant/bedGraphToBigWig.cwl
in:
output_suffix:
valueFrom: .raw.bw
genome_sizes: input_genome_sizes
bed_graph: bedsort_genomecov/bed_file_sorted
scatter: bed_graph
out:
- output_bigwig
bamCoverage-rpkm-trt:
run: ../quant/deeptools-bamcoverage.cwl
scatter: bam
in:
bam: input_trt_bam_files
numberOfProcessors: nthreads
outFileFormat:
valueFrom: bigwig
extendReads:
valueFrom: ${return 200}
normalizeUsing:
valueFrom: RPKM
binSize:
valueFrom: ${return 1}
output_suffix:
valueFrom: .rpkm.bw
out:
- output_bam_coverage
bamCoverage-rpkm-ctrl:
run: ../quant/deeptools-bamcoverage.cwl
in:
bam: input_ctrl_bam_files
numberOfProcessors: nthreads
outFileFormat:
valueFrom: bigwig
extendReads:
valueFrom: ${return 200}
normalizeUsing:
valueFrom: RPKM
binSize:
valueFrom: ${return 1}
output_suffix:
valueFrom: .rpkm.bw
scatter: bam
out:
- output_bam_coverage
bamCompare-ctrl-subtracted-rpkm:
run: ../quant/deeptools-bigwigcompare.cwl
scatterMethod: dotproduct
scatter:
- bigwig1
- bigwig2
in:
numberOfProcessors: nthreads
operation:
valueFrom: subtract
bigwig1: bamCoverage-rpkm-trt/output_bam_coverage
bigwig2: bamCoverage-rpkm-ctrl/output_bam_coverage
binSize:
valueFrom: ${return 1}
outFileFormat:
valueFrom: bigwig
output_suffix:
valueFrom: .ctrl_subtracted.bw
out:
- output
outputs:
bigwig_raw_files:
doc: Raw reads bigWig (signal) files
type: File[]
outputSource: bdg2bw-raw/output_bigwig
bigwig_rpkm_extended_files:
doc: Fragment extended RPKM bigWig (signal) files
type: File[]
outputSource: bamCoverage-rpkm-trt/output_bam_coverage
bigwig_ctrl_subtracted_rpkm_extended_files:
doc: Control subtracted fragment extended RPKM bigWig (signal) files
type: File[]
outputSource: bamCompare-ctrl-subtracted-rpkm/output
bigwig_ctrl_rpkm_extended_files:
doc: Fragment extended RPKM bigWig (signal) control files
type: File[]
outputSource: bamCoverage-rpkm-ctrl/output_bam_coverage
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