add realigner and bqsr

tasks/BQSR.wdl

@@ -0,0 +1,59 @@
+task BQSR {
+  
+  File ref_dir
+  File dbsnp_dir
+  File dbmills_dir
+  
+  String sample
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String fasta
+  String dbsnp
+  String db_mills
+  File realigned_bam
+  File realigned_bam_index
+  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 ${realigned_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 \
+    --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 ${sample}_recal_result.csv
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"  
+  }
+
+  output {
+    File recal_table = "${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 = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
+    File recal_csv = "${sample}_recal_result.csv"
+    File bqsrreport_pdf = "${sample}_bqsr.pdf"
+  }
+}

tasks/Realigner.wdl

@@ -0,0 +1,45 @@
+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} ${sample}.sorted.deduped.realigned.bam
+    
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
+    File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
+
+  }
+}
+
+

workflow.wdl

@@ -1,72 +1,76 @@
+import "./tasks/Realigner.wdl" as Realigner
+import "./tasks/BQSR.wdl" as BQSR
 import "./tasks/PoN.wdl" as PoN
-import "./tasks/mergePoN.wdl" as mergePoN
-	
+  
 workflow {{ project_name }} {
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String panel_id
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String panel_id
 
-	File ref_dir
-	String fasta
-	File cosmic_dir
-	String cosmic_vcf
-	File dbsnp_dir
-	String dbsnp
-	File regions
+  File ref_dir
+  String fasta
+  File cosmic_dir
+  String cosmic_vcf
+  File dbsnp_dir
+  String dbsnp
+  File regions
 
-	Array[Array[File]] normal_recaled_bam_bai
-	String sentieon_docker
-	String cluster_config
-	String disk_size
-	
-	scatter (item in normal_recaled_bam_bai){
-		call PoN.PoN as PoN {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		regions=regions,
-		normal_bam=item[0],
-		normal_bam_index=item[1],
-		cosmic_vcf=cosmic_vcf,
-		cosmic_dir=cosmic_dir,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-		}
-	}
+  Array[Array[File]] normal_recaled_bam_bai
+  String sentieon_docker
+  String cluster_config
+  String disk_size
+  
+  
+  call Realigner.Realigner as Realigner {
+    input:
+    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+    SENTIEON_LICENSE=SENTIEON_LICENSE,
+    fasta=fasta,
+    ref_dir=ref_dir,
+    deduped_bam=Dedup.deduped_bam,
+    deduped_bam_index=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
+  }
 
-	Array[File] TNhaplotyper_pon_vcfs = PoN.TNhaplotyper_pon_vcf
-	Array[File] TNhaplotyper2_pon_vcfs = PoN.TNhaplotyper2_pon_vcf
-	Array[File] TNscope_pon_vcfs = PoN.TNscope_pon_vcf
+  call BQSR.BQSR as BQSR {
+    input:
+    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+    SENTIEON_LICENSE=SENTIEON_LICENSE,
+    fasta=fasta,
+    ref_dir=ref_dir,
+    realigned_bam=Realigner.realigner_bam,
+    realigned_bam_index=Realigner.realigner_bam_index,
+    db_mills=db_mills,
+    dbmills_dir=dbmills_dir,
+    dbsnp=dbsnp,
+    dbsnp_dir=dbsnp_dir,
+    sample=sample_id + '_tumor',
+    docker=sentieon_docker,
+    disk_size=disk_size,
+    cluster_config=cluster_config
+  }
 
-	call mergePoN.mergePoN as mergePoN_TNhaplotyper {
-		input:
-		pon_vcfs=TNhaplotyper_pon_vcfs,
-		panel_id=panel_id,
-		docker=bcftools_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
-
-	call mergePoN.mergePoN as mergePoN_TNhaplotyper2 {
-		input:
-		pon_vcfs=TNhaplotyper2_pon_vcfs,
-		panel_id=panel_id,
-		docker=bcftools_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
-
-	call mergePoN.mergePoN as mergePoN_TNscope {
-		input:
-		pon_vcfs=TNscope_pon_vcfs,
-		panel_id=panel_id,
-		docker=bcftools_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+  call PoN.PoN as PoN {
+    input:
+    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+    SENTIEON_LICENSE=SENTIEON_LICENSE,
+    fasta=fasta,
+    ref_dir=ref_dir,
+    regions=regions,
+    normal_bam=BQSR.recaled_bam,
+    normal_bam_index=BQSR.recaled_bam_index,
+    cosmic_vcf=cosmic_vcf,
+    cosmic_dir=cosmic_dir,
+    dbsnp=dbsnp,
+    dbsnp_dir=dbsnp_dir,
+    docker=sentieon_docker,
+    disk_size=disk_size,
+    cluster_config=cluster_config
+    }
+  }
 }