Update: remove Realigner

tasks/BQSR.wdl

@@ -10,13 +10,13 @@ task BQSR {
   String SENTIEON_LICENSE
   String fasta
   
-  File realigned_bam
-  File realigned_bam_index
+  File deduped_bam
+  File deduped_bam_index
   String docker
   String cluster_config
   String disk_size
 
-  String sample=basename(realigned_bam, ".sorted.deduped.realigned.bam")
+  String sample=basename(deduped_bam, ".sorted.deduped.bam")
 
   command <<<
     set -o pipefail
@@ -25,17 +25,17 @@ task BQSR {
     nt=$(nproc)
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} -i ${realigned_bam} \
+    -r ${ref_dir}/${fasta} -i ${deduped_bam} \
     --algo QualCal \
     -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
     ${sample}_recal_data.table
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} -i ${realigned_bam} -q ${sample}_recal_data.table \
+    -r ${ref_dir}/${fasta} -i ${deduped_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
+    --algo ReadWriter ${sample}.sorted.deduped.recaled.bam
     
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot \
     --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_result.csv
@@ -53,8 +53,8 @@ task BQSR {
   output {
     File recal_table = "${sample}_recal_data.table"
     File recal_post = "${sample}_recal_data.table.post"
-    File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
-    File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
+    File recaled_bam = "${sample}.sorted.deduped.recaled.bam"
+    File recaled_bam_index = "${sample}.sorted.deduped.recaled.bam.bai"
     File recal_csv = "${sample}_recal_result.csv"
     File bqsrreport_pdf = "${sample}_bqsr.pdf"
   }

tasks/PoN.wdl

@@ -12,7 +12,7 @@ task PoN {
   String cluster_config
   String disk_size
 
-  String sample=basename(normal_bam, ".sorted.deduped.realigned.recaled.bam")
+  String sample=basename(normal_bam, ".sorted.deduped.recaled.bam")
   
   command <<<
     set -o pipefail

workflow.wdl

@@ -55,29 +55,14 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call Realigner.Realigner as fastq_Realigner {
-      input:
-      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-      SENTIEON_LICENSE=SENTIEON_LICENSE,
-      fasta=fasta,
-      ref_dir=ref_dir,
-      deduped_bam=fastq_Dedup.deduped_bam,
-      deduped_bam_index=fastq_Dedup.deduped_bam_index,
-      db_mills=db_mills,
-      dbmills_dir=dbmills_dir,
-      docker=sentieon_docker,
-      disk_size=disk_size,
-      cluster_config=cluster_config
-    }
-
     call BQSR.BQSR as fastq_BQSR {
       input:
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       fasta=fasta,
       ref_dir=ref_dir,
-      realigned_bam=fastq_Realigner.realigner_bam,
-      realigned_bam_index=fastq_Realigner.realigner_bam_index,
+      deduped_bam=fastq_Dedup.realigner_bam,
+      deduped_bam_index=fastq_Dedup.realigner_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
@@ -103,7 +88,7 @@ workflow {{ project_name }} {
   }
   
   if (deduped_bam!= "") {
-    call Realigner.Realigner as bam_Realigner {
+    call BQSR.BQSR as bam_BQSR {
       input:
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
@@ -113,21 +98,6 @@ workflow {{ project_name }} {
       deduped_bam_index=deduped_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
-      docker=sentieon_docker,
-      disk_size=disk_size,
-      cluster_config=cluster_config
-    }
-
-    call BQSR.BQSR as bam_BQSR {
-      input:
-      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-      SENTIEON_LICENSE=SENTIEON_LICENSE,
-      fasta=fasta,
-      ref_dir=ref_dir,
-      realigned_bam=bam_Realigner.realigner_bam,
-      realigned_bam_index=bam_Realigner.realigner_bam_index,
-      db_mills=db_mills,
-      dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
       dbsnp_dir=dbsnp_dir,
       docker=sentieon_docker,