#!/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