X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/bcfc5df45a2f51a5736677f5277ce0cb738663e6..9a5debbcb44d46ceff859f5a0f5f968c82d888fa:/cwl/bwa-gatk-wf.cwl

diff --git a/cwl/bwa-gatk-wf.cwl b/cwl/bwa-gatk-wf.cwl
new file mode 100644
index 0000000..675bdd0
--- /dev/null
+++ b/cwl/bwa-gatk-wf.cwl
@@ -0,0 +1,68 @@
+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]