adding helper directory for structure, may reorg later

[arvados-tutorial.git] / cwl / helper / gatk-wf-with-interval.cwl

diff --git a/cwl/helper/gatk-wf-with-interval.cwl b/cwl/helper/gatk-wf-with-interval.cwl
new file mode 100644 (file)
index 0000000..037accd
--- /dev/null
+++ b/cwl/helper/gatk-wf-with-interval.cwl
@@ -0,0 +1,61 @@
+cwlVersion: v1.1
+class: Workflow
+
+requirements:
+  - class: SubworkflowFeatureRequirement
+
+inputs:
+  bam:
+    type: File
+    secondaryFiles:
+      - .bai
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+  sample: string
+  knownsites1:
+    type: File
+    secondaryFiles:
+      - .tbi
+  intervallist:
+    type: File
+
+outputs:
+  gvcf:
+    type: File
+    outputSource: haplotypecaller/gvcf
+
+steps:
+  basecalibrator:
+    run: gatk-baserecalibrator-with-interval.cwl
+    in:
+      bam: bam
+      reference: reference
+      sample: sample
+      knownsites1: knownsites1
+      intervallist: intervallist
+    out: [recaltable]
+  applyBQSR:
+    run: gatk-applyBSQR-with-interval.cwl
+    in: 
+      reference: reference
+      bam: bam
+      sample: sample
+      intervallist: intervallist
+      recaltable: basecalibrator/recaltable
+    out: [recalbam]
+  haplotypecaller:
+    run: gatk-haplotypecaller-with-interval.cwl
+    in:
+      reference: reference
+      bam: applyBQSR/recalbam
+      sample: sample
+      intervallist: intervallist
+    out: [gvcf]