name of bam

tasks/mapping.wdl

@@ -18,7 +18,7 @@ task mapping {
 		set -e	
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}.${type}\tSM:${sample}.${type}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
+		${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}.${type}\tSM:${sample}.${type}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.${type}.sorted.bam -t $nt --sam2bam -i -
 	>>>
 
 	runtime {
@@ -28,7 +28,7 @@ task mapping {
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File sorted_bam = "${sample}.sorted.bam"
-		File sorted_bam_index = "${sample}.sorted.bam.bai"
+		File sorted_bam = "${sample}.${type}.sorted.bam"
+		File sorted_bam_index = "${sample}.${type}.sorted.bam.bai"
 	}
 }