Alter: TNseq input is deduped BAM

tasks/BQSR.wdl

   String fasta
   String dbsnp
   String db_mills
-  File realigned_bam
-  File realigned_bam_index
+  File deduped_bam
+  File deduped_bam_index
   String docker
   String cluster_config
   String disk_size
     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 ${sample}_recal_result.csv
   output {
     File recal_table = "${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/Haplotyper.wdl

   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
   String fasta
-  File recaled_bam
-  File recaled_bam_index
+  File deduped_bam
+  File deduped_bam_index
   File recal_table
   String dbsnp
   String sample
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
 	--interval ${regions} -r ${ref_dir}/${fasta} \
-	-i ${recaled_bam} -q ${recal_table}\
+	-i ${deduped_bam} -q ${recal_table}\
 	--algo Haplotyper -d ${dbsnp_dir}/${dbsnp} \
 	${sample}_hc.vcf
   >>>

tasks/Realigner.wdl

-task Realigner {
-
-  File ref_dir
-  File dbmills_dir
-
-  String SENTIEON_INSTALL_DIR
-  String SENTIEON_LICENSE
-  String sample
-  String fasta
-
-  File deduped_bam
-  File deduped_bam_index
-  String db_mills
-  String docker
-  String cluster_config
-  String disk_size
-  
-  command <<<
-    set -o pipefail
-    set -e
-    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-    nt=$(nproc)
-    
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} \
-    -i ${deduped_bam} \
-    --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
-    
-  >>>
-
-  runtime {
-    docker: docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-  }
-
-  output {
-    File realigned_bam = "${sample}.sorted.deduped.realigned.bam"
-    File realigned_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
-
-  }
-}
-
-

tasks/TNseq.wdl

   String sample
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  File tumor_realigned_bam
-  File tumor_realigned_bam_index
+  File tumor_deduped_bam
+  File tumor_deduped_bam_index
   File tumor_recal_table
-  File normal_realigned_bam
-  File normal_realigned_bam_index
+  File normal_deduped_bam
+  File normal_deduped_bam_index
   File normal_recal_table
   String tumor_name
   String normal_name
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} $INTERVAL \
-    -i ${tumor_realigned_bam} -q ${tumor_recal_table} \
-    -i ${normal_realigned_bam} -q ${normal_recal_table} \
+    -i ${tumor_deduped_bam} -q ${tumor_recal_table} \
+    -i ${normal_deduped_bam} -q ${normal_recal_table} \
     --algo TNhaplotyper2 \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     --germline_vcf ${germline_resource} \

workflow.wdl

 import "./tasks/Metrics.wdl" as Metrics
 import "./tasks/Dedup.wdl" as Dedup
 import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
-import "./tasks/Realigner.wdl" as Realigner
 import "./tasks/BQSR.wdl" as BQSR
 import "./tasks/Haplotyper.wdl" as Haplotyper
 import "./tasks/TNseq.wdl" as TNseq
       cluster_config=cluster_config
     }
 
-    call Realigner.Realigner as tumor_Realigner {
+    call BQSR.BQSR as tumor_BQSR {
       input:
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       deduped_bam_index=tumor_Dedup.deduped_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
-      sample=sample_id + '_tumor',
-      docker=sentieon_docker,
-      disk_size=disk_size,
-      cluster_config=cluster_config
-    }
-
-    call BQSR.BQSR as tumor_BQSR {
-      input:
-      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-      SENTIEON_LICENSE=SENTIEON_LICENSE,
-      fasta=fasta,
-      ref_dir=ref_dir,
-      realigned_bam=tumor_Realigner.realigned_bam,
-      realigned_bam_index=tumor_Realigner.realigned_bam_index,
-      db_mills=db_mills,
-      dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
       dbsnp_dir=dbsnp_dir,
       sample=sample_id + '_tumor',
     cluster_config=cluster_config
   }
 
-  call Realigner.Realigner as normal_Realigner {
+  call BQSR.BQSR as normal_BQSR {
     input:
     SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
     SENTIEON_LICENSE=SENTIEON_LICENSE,
     deduped_bam_index=normal_Dedup.deduped_bam_index,
     db_mills=db_mills,
     dbmills_dir=dbmills_dir,
-    sample=sample_id + '_normal',
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
-  }
-
-  call BQSR.BQSR as normal_BQSR {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    realigned_bam=normal_Realigner.realigned_bam,
-    realigned_bam_index=normal_Realigner.realigned_bam_index,
-    db_mills=db_mills,
-    dbmills_dir=dbmills_dir,
     dbsnp=dbsnp,
     dbsnp_dir=dbsnp_dir,
     sample=sample_id + '_normal',
       sample=sample_id + '_normal',
       fasta=fasta,
       ref_dir=ref_dir,
-      recaled_bam=normal_BQSR.recaled_bam,
-      recaled_bam_index=normal_BQSR.recaled_bam_index,
+      deduped_bam=normal_Dedup.deduped_bam,
+      deduped_bam_index=normal_Dedup.deduped_bam_index,
       recal_table=normal_BQSR.recal_table,
       dbsnp=dbsnp,
       dbsnp_dir=dbsnp_dir,
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       sample=sample_id,
-      normal_realigned_bam=normal_Realigner.realigned_bam,
-      normal_realigned_bam_index=normal_Realigner.realigned_bam_index,
+      normal_deduped_bam=normal_Dedup.deduped_bam,
+      normal_deduped_bam_index=normal_Dedup.deduped_bam_index,
       normal_recal_table=normal_BQSR.recal_table,
-      tumor_realigned_bam=tumor_Realigner.realigned_bam,
-      tumor_realigned_bam_index=tumor_Realigner.realigned_bam_index,
+      tumor_deduped_bam=tumor_Dedup.deduped_bam,
+      tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
       tumor_recal_table=tumor_BQSR.recal_table,
       normal_name=sample_id + "_normal",
       tumor_name=sample_id + "_tumor",