Rearranging for clarity

[arvados-tutorial.git] / cwl / helper / gather-vcf-try2.cwl

diff --git a/cwl/helper/gather-vcf-try2.cwl b/cwl/helper/gather-vcf-try2.cwl
deleted file mode 100644 (file)
index 40a5c9d..0000000
--- a/cwl/helper/gather-vcf-try2.cwl
+++ /dev/null
@@ -1,69 +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:
-  gvcfdir: 
-    type: Directory
-    label: Input directory of gvcfs
-    loadListing: 'shallow_listing'
-  sample: string
-  reference:
-    type: File
-    secondaryFiles:
-      - .amb
-      - .ann
-      - .bwt
-      - .pac
-      - .sa
-      - .fai
-      - ^.dict
-outputs:
-  gatheredgvcf:
-    type: File
-    outputBinding:
-      glob: "*.g.vcf.gz"
-
-baseCommand: /gatk/gatk
-
-arguments:
-  - "--java-options"
-  - "-Xmx8G" 
-  - GatherVcfs
-  - shellQuote: false
-    valueFrom: >
-    ${
-    var samples = [];
-    for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
-      var name = inputs.gvcfdir.listing[i];
-      if (name.nameext ==='.gz' ) {
-        samples.push(name.basename);
-      }
-    }
-    samples = samples.sort();
-    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