Update output

tasks/varscan.wdl

 
 
     command <<<
-        samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3  --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
+        samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
     >>>
 
     runtime {
         dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
     }
     output {
-        File varscan_snp = "${sample}.VarScan.TN.SNP"
-        File varscan_indel = "${sample}.VarScan.TN.INDEL"
+        File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
+        File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
         
     }
 }