Rearranging for clarity

[arvados-tutorial.git] / WGS-processing / cwl / helper / gather-array-vcf.cwl

diff --git a/WGS-processing/cwl/helper/gather-array-vcf.cwl b/WGS-processing/cwl/helper/gather-array-vcf.cwl
new file mode 100644 (file)
index 0000000..d566841
--- /dev/null
+++ b/WGS-processing/cwl/helper/gather-array-vcf.cwl
@@ -0,0 +1,85 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Gathering vcf using Picard 
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: broadinstitute/gatk:4.1.7.0
+  ShellCommandRequirement: {}
+  InlineJavascriptRequirement: {}
+
+hints:
+  ResourceRequirement:
+    ramMin: 20000
+    coresMin: 4    
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+
+inputs:
+  gvcfarray: 
+    type: File[] 
+  sample: string
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+outputs:
+  gatheredgvcf:
+    type: File
+    secondaryFiles:
+      - .tbi
+    outputBinding:
+      glob: "*.g.vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+  - "--java-options"
+  - "-Xmx8G" 
+  - MergeVcfs
+  - shellQuote: false
+    valueFrom: | 
+     ${function compare(a, b) {
+      var baseA = a.basename;
+      var baseB = b.basename;
+
+      var comparison = 0;
+      if (baseA > baseB) {
+      comparison = 1;
+      } else if (baseA < baseB) {
+      comparison = -1;
+      }
+      return comparison;
+      }
+
+      var sortedarray = [];
+      sortedarray = inputs.gvcfarray.sort(compare)
+ 
+      var samples = [];
+      for (var i = 0; i < sortedarray.length; i++) {
+        var name = sortedarray[i];
+        if (name.nameext ==='.gz' ) {
+          samples.push(name.path);
+        }
+      }
+     
+      var sampleinput = "";
+
+      for (var i = 0; i < samples.length; i++) {
+       var s1 = samples[i];
+       sampleinput = sampleinput + "-I " + s1 + " "
+      }
+    
+      return sampleinput;
+      }
+  - prefix: "-O"
+    valueFrom: $(inputs.sample).g.vcf.gz