adding helper directory for structure, may reorg later

[arvados-tutorial.git] / cwl / helper / gatk-splitintervals.cwl

diff --git a/cwl/helper/gatk-splitintervals.cwl b/cwl/helper/gatk-splitintervals.cwl
new file mode 100644 (file)
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--- /dev/null
+++ b/cwl/helper/gatk-splitintervals.cwl
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+cwlVersion: v1.1
+class: CommandLineTool
+label: Creating interval files for scattering
+
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: broadinstitute/gatk:4.1.7.0
+
+hints:
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+    keep_cache: 1024
+  ResourceRequirement:
+    ramMin: 5000
+    coresMin: 2
+
+inputs:
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+  sample: string
+  scattercount: string
+ 
+outputs:
+  intervalfiles:
+    type: File[]
+    outputBinding:
+      glob: "intervalfiles/*.interval_list"
+
+baseCommand: /gatk/gatk
+
+arguments:
+  - "--java-options"
+  - "-Xmx4G"
+  - SplitIntervals
+  - prefix: "-R"
+    valueFrom: $(inputs.reference)
+  - prefix: "--scatter-count"
+    valueFrom: $(inputs.scattercount)
+  - prefix: "--subdivision-mode"
+    valueFrom: "BALANCING_WITHOUT_INTERVAL_SUBDIVISION"
+  - prefix: "-O"
+    valueFrom: "intervalfiles"