--- /dev/null
+cwlVersion: v1.1
+class: Workflow
+
+inputs:
+ fastq1: File
+ fastq2: File
+ reference:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ - ^.dict
+ sample: string
+
+outputs:
+ qc-html:
+ type: File[]
+ outputSource: fastqc/out-html
+ qc-zip:
+ type: File[]
+ outputSource: fastqc/out-zip
+ vcf:
+ type: File
+ outputSource: vep/out-vcf
+
+steps:
+ fastqc:
+ run: fastqc.cwl
+ in:
+ fastq1: fastq1
+ fastq2: fastq2
+ out: [out-html, out-zip]
+ bwamem-samtools-view:
+ run: bwamem-samtools-view.cwl
+ in:
+ fastq1: fastq1
+ fastq2: fastq2
+ reference: reference
+ sample: sample
+ out: [bam]
+ samtools-sort:
+ run: samtools-sort.cwl
+ in:
+ bam: bwamem-samtools-view/bam
+ sample: sample
+ out: [out]
+ samtools-index:
+ run: samtools-index.cwl
+ in:
+ bam: samtools-sort/out
+ out: [out]
+ haplotypecaller:
+ run: gatk-haplotypecaller.cwl
+ in:
+ reference: reference
+ bam: samtools-index/out
+ sample: sample
+ out: [vcf]
+ vep:
+ run: vep.cwl
+ in:
+ vcf: haplotypecaller/vcf
+ sample: sample
+ out: [out-vcf]