update varscan.wdl

tasks/varscan.wdl

@@ -13,9 +13,7 @@ task varscan {
 
 
     command <<<
-        samtools mpileup -q 1 -f ${ref_dir}/${fasta} ${normal_bam} > normal_pileup
-        samtools mpileup -q 1 -f ${ref_dir}/${fasta} ${tumor_bam} > tumor_pileup
-        java -jar VarScan.v2.4.3.jar somatic normal_pileup tumor_pileup --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 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 {