Create printReads.cwl

Author: FarahZKhan

tools/printReads.cwl

@@ -0,0 +1,93 @@
+#!/usr/bin/env cwl-runner
+#
+# Authors: [email protected] and [email protected] UNIVERSITY OF MELBOURNE
+# Developed for CWL consortium http://commonwl.org/
+
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+
+description: |
+  Prints all reads that have a mapping quality above zero
+  Usage: java -Xmx4g -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input1.bam -I input2.bam -o output.bam --read_filter MappingQualityZero
+  Options: 
+   -T PrintReads Tool name to be executed
+   -R reference.fasta Reference sequence in fasta format
+   -I input.bam bam file produce from indelRealigner
+   -BQSR recalibration_report.grp the recalibration table data in recalibration_report.grp produced by BaseRecalibration to recalibrate the quality scores in input.bam
+   -o output.bam Output file name
+
+requirements:
+  - import: node-engine.cwl
+  - import: envvar-global.cwl
+  - import: gatk-docker.cwl
+
+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: "#printReads"
+    type: string
+    default: "PrintReads"
+    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_printReads"
+    type: File
+    description: bam file produced after indelRealigner
+    inputBinding:
+      position: 5 
+      prefix: "-I"
+      secondaryFiles:
+        - "^.bai"
+      
+  - id: "#input_baseRecalibrator"
+    type: File
+    description: the recalibration table produced by BaseRecalibration
+    inputBinding:
+      position: 5 
+      prefix: "-BQSR"
+      
+  - id: "#outputfile_printReads"
+    type: string
+    description: name of the output file from indelRealigner
+    inputBinding:
+      position: 9
+      prefix: "-o"
+    
+outputs:
+  - id: "#output_printReads"
+    type: File
+    outputBinding: 
+      glob:
+        engine: cwl:JsonPointer
+        script: /job/outputfile_printReads
+
+baseCommand: ["java"]
+