Merge pull request #34 from FarahZKhan/patch-4

Create haplotypeCaller.cwl

Author: portah

tools/GATK-haplotypeCaller.cwl

@@ -0,0 +1,91 @@
+#!/usr/bin/env cwl-runner
+#
+# Authors: [email protected] and [email protected] UNIVERSITY OF MELBOURNE
+# Developed for CWL consortium http://commonwl.org/
+class: CommandLineTool
+
+description: |
+  Call germline SNPs and indels via local re-assembly of haplotypes
+  Options:
+    -R reference.fasta Reference sequence in fasta format
+    -T HaplotypeCaller Tool name to be executed
+    -I sample.bam bam file from printReads
+    [--dbsnp dbSNP.vcf] latest_dbsnp.vcf set of known indels
+    [-stand_call_conf 30] The minimum phred-scaled confidence threshold at which variants should be called - optional
+    [-stand_emit_conf 10] The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold) - optonal
+    [-L targets.interval_list] target bed file - if any
+    -o output.raw.snps.indels.vcf  Output file from haplotypr caller
+   
+requirements:
+  - import: node-engine.cwl
+  - import: envvar-global.cwl
+  - import: gatk-docker.cwl
+arguments:
+  - valueFrom: "/home/biodocker/bin/gatk/target/GenomeAnalysisTK.jar"
+    position: 2
+    prefix: "-jar"
+    
+inputs:
+
+  - id: "#java_arg"
+    type: string
+    default: "-Xmx4g"
+    inputBinding: 
+      position: 1
+
+  - id: "#HaplotypeCaller"
+    type: string
+    default: "HaplotypeCaller"
+    inputBinding: { position: 3, prefix: "-T" }
+    description: tool used for this step from GATK jar
+     
+  - id: "#reference"
+    type: File
+    inputBinding:
+      position: 4
+      prefix: "-R"
+      secondaryFiles:
+        - ".amb"
+        - ".ann"
+        - ".bwt"
+        - ".pac"
+        - ".rbwt"
+        - ".rpac"
+        - ".rsa"
+        - ".sa"
+        - ".fai"
+        - "^.dict"
+        
+  - id: "#inputBam_HaplotypeCaller"
+    type: File
+    description: bam file produced after printReads
+    inputBinding:
+      position: 5 
+      prefix: "-I"
+      secondaryFiles:
+        - "^.bai"      
+    
+  - id: "#dbsnp"  
+    type: File
+    description: latest_dbsnp.vcf set of known indels
+    inputBinding: 
+      position: 6
+      prefix: "--dbsnp"
+      
+  - id: "#outputfile_HaplotypeCaller"
+    type: string
+    description: name of the output file from HaplotypeCaller
+    inputBinding:
+      position: 7
+      prefix: "-o"
+    
+outputs:
+  - id: "#output_HaplotypeCaller"
+    type: File
+    outputBinding: 
+      glob:
+        engine: cwl:JsonPointer
+        script: /job/outputfile_HaplotypeCaller
+
+baseCommand: ["java"]
+