Fix bug: processSomatic output

tasks/processSomatic.wdl

@@ -1,37 +1,40 @@
 task processSomatic {
     
-	String sample
-	File varscan_snp
-	File varscan_indel
-	
+    String sample
+    File varscan_snp
+    File varscan_indel
+    
     String docker
     String cluster_config
     String disk_size
 
-	command <<<
-		java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${varscan_snp}
-		java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${varscan_indel}
-	>>>
+    command <<<
+        cp ${varscan_snp} ./
+        cp ${varscan_indel} ./
+        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf
+        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf
+
+    >>>
 
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
+    runtime {
+        docker: docker
+        cluster: cluster_config
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
 
-	output {
-		File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
-		File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
-		File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
-		File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
-		File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
-		File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
-		File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
-		File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
-		File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
-		File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
-		File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
-		File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
-	}
+    output {
+        File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
+        File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
+        File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
+        File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
+        File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
+        File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
+        File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
+        File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
+        File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
+        File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
+        File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
+        File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
+    }
 }