Rearranging for clarity

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

diff --git a/cwl/helper/gatk-haplotypecaller.cwl b/cwl/helper/gatk-haplotypecaller.cwl
deleted file mode 100644 (file)
index 1169f45..0000000
--- a/cwl/helper/gatk-haplotypecaller.cwl
+++ /dev/null
@@ -1,66 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Germline variant calling using GATK with output gvcf
-
-$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
-
-outputs:
-  gvcf:
-    type: File
-    outputBinding:
-      glob: "*vcf.gz"
-
-baseCommand: /gatk/gatk
-
-arguments:
-  - "--java-options"
-  - "-Xmx4G" 
-  - HaplotypeCaller
-  - prefix: "-R"
-    valueFrom: $(inputs.reference)
-  - prefix: "-I"
-    valueFrom: $(inputs.bam)
-  - prefix: "-O"
-    valueFrom: $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
-  - prefix: "-ERC"
-    valueFrom: "GVCF"
-  - prefix: "-GQB"
-    valueFrom: "5"
-  - prefix: "-GQB"
-    valueFrom: "20"
-  - prefix: "-GQB"
-    valueFrom: "60"