-cwlVersion: v1.1
-class: Workflow
-
-requirements:
- - class: SubworkflowFeatureRequirement
-
-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: haplotypecaller/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]