X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/aa289173560cd4466d890f3a63927650e37d8aa7..cec9a7f6a83fc2596e042e8adc6179b202f92a6e:/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl

diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
new file mode 100644
index 0000000..41cfd2e
--- /dev/null
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -0,0 +1,68 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Applying base quality score recalibration 
+
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: broadinstitute/gatk:4.1.7.0
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.bam)
+
+hints:
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+    keep_cache: 1024
+  ResourceRequirement:
+    ramMin: 5000
+    coresMin: 2
+
+inputs:
+  bam:
+    type: File
+    secondaryFiles:
+      - .bai
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+  sample: string
+  recaltable: 
+    type: File
+  intervallist:
+    type: File
+
+outputs:
+  recalbam:
+    type: File
+    secondaryFiles: 
+      - .bai
+    outputBinding:
+      glob: "*nodups_BQSR.bam"
+
+baseCommand: /gatk/gatk
+
+arguments:
+  - "--java-options"
+  - "-Xmx4G"
+  - ApplyBQSR
+  - prefix: "-R"
+    valueFrom: $(inputs.reference)
+  - prefix: "-I"
+    valueFrom: $(inputs.bam.basename)
+  - prefix: "--bqsr-recal-file"
+    valueFrom: $(inputs.recaltable)
+  - prefix: "-L"
+    valueFrom: $(inputs.intervallist)
+  - prefix: "-O"
+    valueFrom: $(inputs.sample)nodups_BQSR.bam