Fix bug: BQSR.wdl

tasks/BQSR.wdl

@@ -8,7 +8,6 @@ task BQSR {
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
   String fasta
-  File? regions
   String dbsnp
   String db_mills
   File realigned_bam
@@ -22,17 +21,18 @@ task BQSR {
     set -e
     export SENTIEON_LICENSE=${SENTIEON_LICENSE}
     nt=$(nproc)
-    if [ ${regions} != "" ]; then
-      ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} --interval ${regions} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
-    else
-      ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
-    fi
 
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} -q ${sample}_recal_data.table --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.realigned.recaled.bam
-
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
-
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon plot bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} -i ${realigned_bam} \
+    -q ${sample}_recal_data.table --algo QualCal \
+    -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
+    ${sample}_recal_data.table.post \
+    --algo ReadWriter ${sample}.sorted.deduped.realigned.recaled.bam
+    
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot \
+    --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_result.csv
+    
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsr.pdf ${sample}_recal_result.csv
   >>>
 
   runtime {
@@ -47,7 +47,7 @@ task BQSR {
     File recal_post = "${sample}_recal_data.table.post"
     File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
     File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
-    File recal_csv = "${sample}_recal_data.csv"
-    File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
+    File recal_csv = "${sample}_recal_result.csv"
+    File bqsrreport_pdf = "${sample}_bqsr.pdf"
   }
 }

tasks/Realigner.wdl

@@ -23,7 +23,7 @@ task Realigner {
     nt=$(nproc)
     
     if [ ${regions} ]; then
-      INTERVAL="--interval ${regions}"
+      INTERVAL="--interval_list ${regions}"
     else
       INTERVAL=""
     fi

workflow.wdl

@@ -137,7 +137,6 @@ workflow {{ project_name }} {
       dbsnp=dbsnp,
       dbsnp_dir=dbsnp_dir,
       sample=sample_id + '_tumor',
-      regions=regions,
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_config
@@ -232,7 +231,6 @@ workflow {{ project_name }} {
     dbsnp=dbsnp,
     dbsnp_dir=dbsnp_dir,
     sample=sample_id + '_normal',
-    regions=regions,
     docker=sentieon_docker,
     disk_size=disk_size,
     cluster_config=cluster_config