更新 'tasks/TNseq.wdl'

tasks/TNseq.wdl

@@ -11,8 +11,6 @@ task sentieon_TNseq{
     String ref_fasta
     File germline_resource
     File germline_resource_tbi
-    File? regions
-    Int? interval_padding
 
     # excute env
     String docker
@@ -27,10 +25,6 @@ task sentieon_TNseq{
         export SENTIEON_LICENSE=${SENTIEON_LICENSE}
         nt=$(nproc)
 
-        if [${regions}]; then
-            INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
-        else
-            INTERVAL=""
         fi
 
         if [${normal_bam}];then
@@ -42,7 +36,7 @@ task sentieon_TNseq{
         fi
 
         sentieon driver -t $nt -r ${ref_dir}/${ref_fasta} \
-        $INPUT $INTERVAL \
+        $INPUT \
         --algo TNhaplotyper2 $SAMPLE \
         --germline_vcf ${germline_resource} \
         ${sample_id}.TNseq.raw.vcf \