feat: bqsr interval

tasks/BQSR.wdl

@@ -15,14 +15,24 @@ task BQSR {
   String cluster_config
   String disk_size
 
+  File? regions
+  Int? interval_padding
+  
   command <<<
     set -o pipefail
     set -e
     export SENTIEON_LICENSE=${SENTIEON_LICENSE}
     nt=$(nproc)
 
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+
     sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} -i ${deduped_bam} \
+    $INTERVAL \
     --algo QualCal \
     -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
     ${sample}_recal_data.table

workflow.wdl

@@ -97,11 +97,11 @@ workflow {{ project_name }} {
     call Metrics.Metrics as tumor_Metrics {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.T',
       fasta=fasta,
       ref_dir=ref_dir,
       sorted_bam=tumor_mapping.sorted_bam,
       sorted_bam_index=tumor_mapping.sorted_bam_index,
-      sample=sample_id + '.T',
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_16cpu_32gb
@@ -110,9 +110,9 @@ workflow {{ project_name }} {
     call Dedup.Dedup as tumor_Dedup {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.T',
       sorted_bam=tumor_mapping.sorted_bam,
       sorted_bam_index=tumor_mapping.sorted_bam_index,
-      sample=sample_id + '.T',
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_16cpu_32gb
@@ -121,11 +121,11 @@ workflow {{ project_name }} {
     call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.T',
       fasta=fasta,
       ref_dir=ref_dir,
       deduped_bam=tumor_Dedup.deduped_bam,
       deduped_bam_index=tumor_Dedup.deduped_bam_index,
-      sample=sample_id + '.T',
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_16cpu_32gb
@@ -134,6 +134,7 @@ workflow {{ project_name }} {
     call BQSR.BQSR as tumor_BQSR {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.T',
       fasta=fasta,
       ref_dir=ref_dir,
       deduped_bam=tumor_Dedup.deduped_bam,
@@ -142,7 +143,8 @@ workflow {{ project_name }} {
       dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
       dbsnp_dir=dbsnp_dir,
-      sample=sample_id + '.T',
+      regions=regions,
+      interval_padding=interval_padding,
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_16cpu_32gb
@@ -205,11 +207,11 @@ workflow {{ project_name }} {
     call Metrics.Metrics as normal_Metrics {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.N',
       fasta=fasta,
       ref_dir=ref_dir,
       sorted_bam=normal_mapping.sorted_bam,
       sorted_bam_index=normal_mapping.sorted_bam_index,
-      sample=sample_id + '.N',
       regions=regions,
       docker=sentieon_docker,
       disk_size=disk_size,
@@ -219,9 +221,9 @@ workflow {{ project_name }} {
     call Dedup.Dedup as normal_Dedup {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.N',
       sorted_bam=normal_mapping.sorted_bam,
       sorted_bam_index=normal_mapping.sorted_bam_index,
-      sample=sample_id + '.N',
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_16cpu_32gb
@@ -230,11 +232,11 @@ workflow {{ project_name }} {
     call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.N',
       fasta=fasta,
       ref_dir=ref_dir,
       deduped_bam=normal_Dedup.deduped_bam,
       deduped_bam_index=normal_Dedup.deduped_bam_index,
-      sample=sample_id + '.N',
       regions=regions,
       docker=sentieon_docker,
       disk_size=disk_size,
@@ -244,6 +246,7 @@ workflow {{ project_name }} {
     call BQSR.BQSR as normal_BQSR {
       input:
       SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id + '.N',
       fasta=fasta,
       ref_dir=ref_dir,
       deduped_bam=normal_Dedup.deduped_bam,
@@ -252,7 +255,8 @@ workflow {{ project_name }} {
       dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
       dbsnp_dir=dbsnp_dir,
-      sample=sample_id + '.N',
+      regions=regions,
+      interval_padding=interval_padding,
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_16cpu_32gb