Merge pull request common-workflow-library#39 from FarahZKhan/patch-10

Update GATK-realignTargetCreator.cwl

tools/GATK-realignTargetCreator.cwl

@@ -1,15 +1,15 @@
 #!/usr/bin/env cwl-runner
 #
-# To use it as stand alone tool - example: "cwltool realignerTargerCreator.cwl realignerTargerCreator.json"
-#
+# To use it as stand alone tool - example: "cwltool --tmpdir-prefix="$(pwd)"/name_of_tmpDir/ --tmp-outdir-prefix="$(pwd)"/name_of_tmpDir/ ./realignTargetCreator.cwl ./realignTargetCreator.json"
+
 # Authors: [email protected] and [email protected] UNIVERSITY OF MELBOURNE
 # Developed for CWL consortium http://commonwl.org/
 
 class: CommandLineTool
 
 description: |
   This is a tool wrapper for GATK tool called realignerTargetCreator. It accepts 3 input files and produces a file containing list of target intervals to pass to the IndelRealigner.
-  Usage: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I inout.bam --known indels.vcf -o forIndelRealigner.intervals 
+  Usage: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I input.bam --known indels.vcf -o forIndelRealigner.intervals 
   Options: 
     -T tool Tool name to be executed
     -R File Reference sequence in fasta format
@@ -20,29 +20,44 @@ requirements:
   - import: node-engine.cwl
   - import: envvar-global.cwl
   - import: gatk-docker.cwl
+  - class: CreateFileRequirement
+    fileDef:
+      - filename:
+          engine: node-engine.cwl
+          script: $job['inputBam_realign'].path.split('/').slice(-1)[0]
+        fileContent:
+          engine: "cwl:JsonPointer"
+          script: /job/inputBam_realign
+
+arguments:
+  - valueFrom: "/tmp/job_tmp"
+    position: 2
+    separate: false
+    prefix: "-Djava.io.tmpdir="
+
+  - valueFrom: "/home/biodocker/bin/gatk/target/GenomeAnalysisTK.jar"
+    position: 3
+    prefix: "-jar"
 
 inputs:
+
   - id: "#java_arg"
     type: string
     default: "-Xmx4g"
     inputBinding: 
       position: 1
-
-  - id: "#jar_file"
-    type: string
-    inputBinding: { position: 2, prefix: "-jar" }
-    description: GATK jar file
 
   - id: "#RealignerTarget"
     type: string
     default: "RealignerTargetCreator"
-    inputBinding: { position: 3, prefix: "-T" }
+    inputBinding: { position: 4, prefix: "-T" }
     description: tool used for this step from GATK jar
+
 
   - id: "#reference"
     type: File
     inputBinding:
-      position: 4
+      position: 5
       prefix: "-R"
       secondaryFiles:
         - ".amb"
@@ -60,25 +75,26 @@ inputs:
     type: File
     description: bam file produced after mark-duplicates execution
     inputBinding:
-      position: 5 
+      position: 6
       prefix: "-I"
       secondaryFiles:
-        - ".bai"
-        
+        - "^.bai"
+
   - id: "#known"  
     type:
       type: array
       items: File
       inputBinding: { prefix: "--known" }
-    inputBinding:  position: 6
+    inputBinding: 
+      position: 7
 
   - id: "#outputfile_realignTarget"
     type: string
     description: name of the output file from realignTargetCreator
     inputBinding:
-      position: 9
+      position: 8
       prefix: "-o"
-        
+
 outputs:
   - id: "#output_realignTarget"
     type: File