Fix bug: TNseq.wdl

tasks/Realigner.wdl

@@ -8,7 +8,6 @@ task Realigner {
   String sample
   String fasta
 
-  File? regions
   File Dedup_bam
   File Dedup_bam_index
   String db_mills
@@ -22,14 +21,8 @@ task Realigner {
     export SENTIEON_LICENSE=${SENTIEON_LICENSE}
     nt=$(nproc)
     
-    if [ ${regions} ]; then
-      INTERVAL="--interval_list ${regions}"
-    else
-      INTERVAL=""
-    fi
-    
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} $INTERVAL \
+    -r ${ref_dir}/${fasta} \
     -i ${Dedup_bam} \
     --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
     

tasks/TNseq.wdl

@@ -60,7 +60,8 @@ task TNseq {
     --tumor_segments ${sample}.contamination.segments \
     ${sample}.contamination
     
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r REFERENCE \
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} \
     --algo TNfilter \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     -v ${sample}.TNseq.TN.tmp.vcf \

workflow.wdl

@@ -214,7 +214,6 @@ workflow {{ project_name }} {
     sample=sample_id + '_normal',
     docker=sentieon_docker,
     disk_size=disk_size,
-    regions=regions,
     cluster_config=cluster_config
   }