更新 'tasks/manta.wdl'

tasks/manta.wdl

@@ -16,9 +16,13 @@ task manta_calling{
     command <<<
     set -exo pipefail
     nt=$(nproc)
+    if [ ${normal_bam} ]; then
+      INPUT="--normalBam ${normal_bam} --tumorBam ${tumor_bam}"
+    else
+      INPUT="--tumorBam ${tumor_bam}"
+    fi
     /home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \
-    --normalBam ${normal_bam} \
-    --tumorBam ${tumor_bam} \
+    $INPUT \
     --referenceFasta ${ref_dir}/${ref_fasta} \
     --runDir ${out_dir}
     
@@ -28,7 +32,12 @@ task manta_calling{
 
     ls ${out_dir}
 
-    tar cvf ${out_dir}.tar ${out_dir}
+    if [ ${normal_bam} ]; then
+      cp ${out_dir}/results/variants/somaticSV.vcf.gz ${sample_id}.Manta.somaticSV.vcf.gz
+      cp ${out_dir}/results/variants/diploidSV.vcf.gz ${sample_id}.Manta.germlineSV.vcf.gz
+    else
+      cp ${out_dir}/results/variants/tumorSV.vcf.gz ${sample_id}.Manta.somaticSV.vcf.gz
+    fi
     >>>
 
     runtime{
@@ -40,8 +49,7 @@ task manta_calling{
     }
 
     output{
-        File out_file = "${out_dir}.tar"
-        File manta_indel_vcf = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz"
-        File manta_indel_vcf_index = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz.tbi"
+    	File somatic_vcf = "${sample}.Manta.somaticSV.vcf.gz"
+    	File? germline_vcf = "${sample}.Manta.germlineSV.vcf.gz"
     }
 }