Updating readme and reorganization

[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
deleted file mode 100644 (file)
index d566841..0000000
--- a/WGS-processing/cwl/helper/gather-array-vcf.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-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