Alter: BQSR

tasks/BQSR.wdl

@@ -27,6 +27,16 @@ task BQSR {
     --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 ${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.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
   >>>
 
   runtime {
@@ -38,5 +48,10 @@ task BQSR {
 
   output {
     File recal_table = "${sample}_recal_data.table"
+    File recal_post = "${sample}_recal_data.table.post"
+    File recaled_bam = "${sample}.sorted.deduped.recaled.bam"
+    File recaled_bam_index = "${sample}.sorted.deduped.recaled.bam.bai"
+    File recal_csv = "${sample}_recal_data.csv"
+    File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
   }
 }

tasks/Haplotyper.wdl

@@ -6,9 +6,8 @@ task Haplotyper {
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
   String fasta
-  File deduped_bam
-  File deduped_bam_index
-  File recal_table
+  File recaled_bam
+  File recaled_bam_index
   String dbsnp
   String sample
   String docker
@@ -31,10 +30,10 @@ task Haplotyper {
     fi
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-	--interval ${regions} -r ${ref_dir}/${fasta} \
-	-i ${deduped_bam} -q ${recal_table}\
-	--algo Haplotyper -d ${dbsnp_dir}/${dbsnp} \
-	${sample}_hc.vcf
+    --interval ${regions} -r ${ref_dir}/${fasta} \
+    -i ${recaled_bam} \
+    --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} \
+    ${sample}_hc.vcf
   >>>
   
   runtime {

tasks/TNscope.wdl

@@ -3,12 +3,10 @@ task TNscope {
   String sample
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  File tumor_deduped_bam
-  File tumor_deduped_bam_index
-  File tumor_recal_table
-  File normal_deduped_bam
-  File normal_deduped_bam_index
-  File normal_recal_table
+  File tumor_recaled_bam
+  File tumor_recaled_bam_index
+  File normal_recaled_bam
+  File normal_recaled_bam_index
   String tumor_name
   String normal_name
 
@@ -45,8 +43,7 @@ task TNscope {
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} $INTERVAL \
-    -i ${tumor_deduped_bam} -q ${tumor_recal_table} \
-    -i ${normal_deduped_bam} -q ${normal_recal_table} \
+    -i ${tumor_recaled_bam} -i ${normal_recaled_bam} \
     --algo TNscope \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     --dbsnp ${dbsnp_dir}/${dbsnp} \

tasks/TNseq.wdl

@@ -3,12 +3,10 @@ task TNseq {
   String sample
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  File tumor_deduped_bam
-  File tumor_deduped_bam_index
-  File tumor_recal_table
-  File normal_deduped_bam
-  File normal_deduped_bam_index
-  File normal_recal_table
+  File tumor_recaled_bam
+  File tumor_recaled_bam_index
+  File normal_recaled_bam
+  File normal_recaled_bam_index
   String tumor_name
   String normal_name
 
@@ -45,8 +43,7 @@ task TNseq {
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} $INTERVAL \
-    -i ${tumor_deduped_bam} -q ${tumor_recal_table} \
-    -i ${normal_deduped_bam} -q ${normal_recal_table} \
+    -i ${tumor_recaled_bam} -i ${normal_recaled_bam} \
     --algo TNhaplotyper2 \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     --germline_vcf ${germline_resource} \

workflow.wdl

@@ -231,9 +231,8 @@ workflow {{ project_name }} {
         sample=sample_id + '_normal',
         fasta=fasta,
         ref_dir=ref_dir,
-        deduped_bam=normal_Dedup.deduped_bam,
-        deduped_bam_index=normal_Dedup.deduped_bam_index,
-        recal_table=normal_BQSR.recal_table,
+        recaled_bam=normal_BQSR.recaled_bam,
+        recaled_bam_index=normal_BQSR.recaled_bam_index,
         dbsnp=dbsnp,
         dbsnp_dir=dbsnp_dir,
         regions=regions,
@@ -249,12 +248,10 @@ workflow {{ project_name }} {
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         sample=sample_id,
-        normal_deduped_bam=normal_Dedup.deduped_bam,
-        normal_deduped_bam_index=normal_Dedup.deduped_bam_index,
-        normal_recal_table=normal_BQSR.recal_table,
-        tumor_deduped_bam=tumor_Dedup.deduped_bam,
-        tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
-        tumor_recal_table=tumor_BQSR.recal_table,
+        normal_recaled_bam=normal_BQSR.recaled_bam,
+        normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+        tumor_recaled_bam=tumor_BQSR.recaled_bam,
+        tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
         normal_name=sample_id + "_normal",
         tumor_name=sample_id + "_tumor",
         fasta=fasta,
@@ -310,12 +307,10 @@ workflow {{ project_name }} {
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         sample=sample_id,
-        normal_deduped_bam=normal_Dedup.deduped_bam,
-        normal_deduped_bam_index=normal_Dedup.deduped_bam_index,
-        normal_recal_table=normal_BQSR.recal_table,
-        tumor_deduped_bam=tumor_Dedup.deduped_bam,
-        tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
-        tumor_recal_table=tumor_BQSR.recal_table,
+        normal_recaled_bam=normal_BQSR.recaled_bam,
+        normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+        tumor_recaled_bam=tumor_BQSR.recaled_bam,
+        tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
         normal_name=sample_id + "_normal",
         tumor_name=sample_id + "_tumor",
         fasta=fasta,
@@ -369,10 +364,10 @@ workflow {{ project_name }} {
       call somatic.somatic as somatic {
         input:
         sample=sample_id,
-        tumor_bam=tumor_Dedup.deduped_bam,
-        tumor_bam_index=tumor_Dedup.deduped_bam_index,
-        normal_bam=normal_Dedup.deduped_bam,
-        normal_bam_index=normal_Dedup.deduped_bam_index,
+        normal_bam=normal_BQSR.recaled_bam,
+        normal_bam_index=normal_BQSR.recaled_bam_index,
+        tumor_bam=tumor_BQSR.recaled_bam,
+        tumor_bam_index=tumor_BQSR.recaled_bam_index,
         ref_dir=ref_dir,
         fasta=fasta,    
         docker=varscan_docker,
@@ -444,7 +439,7 @@ workflow {{ project_name }} {
 
   if (input_bam) {
     if (tumor_deduped_bam != "") {
-      call BQSR.BQSR as tumor_BQSR {
+      call BQSR.BQSR as tumor_BQSR_fb {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
@@ -464,7 +459,7 @@ workflow {{ project_name }} {
     }
     
     if (normal_deduped_bam != "") {
-      call BQSR.BQSR as normal_BQSR {
+      call BQSR.BQSR as normal_BQSR_fb {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
@@ -484,16 +479,15 @@ workflow {{ project_name }} {
     }
     
     if (haplotyper) {
-      call Haplotyper.Haplotyper as Haplotyper {
+      call Haplotyper.Haplotyper as Haplotyper_fb {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         sample=sample_id + '_normal',
         fasta=fasta,
         ref_dir=ref_dir,
-        deduped_bam=normal_Dedup.deduped_bam,
-        deduped_bam_index=normal_Dedup.deduped_bam_index,
-        recal_table=normal_BQSR.recal_table,
+        recaled_bam=normal_BQSR_fb.recaled_bam,
+        recaled_bam_index=normal_BQSR_fb.recaled_bam_index,
         dbsnp=dbsnp,
         dbsnp_dir=dbsnp_dir,
         regions=regions,
@@ -504,17 +498,15 @@ workflow {{ project_name }} {
     }
     
     if (tnseq) {
-      call TNseq.TNseq as TNseq {
+      call TNseq.TNseq as TNseq_fb {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         sample=sample_id,
-        normal_deduped_bam=normal_Dedup.deduped_bam,
-        normal_deduped_bam_index=normal_Dedup.deduped_bam_index,
-        normal_recal_table=normal_BQSR.recal_table,
-        tumor_deduped_bam=tumor_Dedup.deduped_bam,
-        tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
-        tumor_recal_table=tumor_BQSR.recal_table,
+        normal_recaled_bam=normal_BQSR_fb.recaled_bam,
+        normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,
+        tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,
+        tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,
         normal_name=sample_id + "_normal",
         tumor_name=sample_id + "_tumor",
         fasta=fasta,
@@ -530,9 +522,9 @@ workflow {{ project_name }} {
       }
 
       if (annovar) {
-        call ANNOVAR.ANNOVAR as TNseq_annovar {
+        call ANNOVAR.ANNOVAR as TNseq_annovar_fb {
           input:
-          vcf=TNseq.TNseq_vcf,
+          vcf=TNseq_fb.TNseq_vcf,
           hg=hg,
           only_pass=only_pass,
           annovar_database=annovar_database,
@@ -543,9 +535,9 @@ workflow {{ project_name }} {
       }
 
       if (vep) {
-        call VEP.VEP as TNseq_VEP {
+        call VEP.VEP as TNseq_VEP_fb {
           input: 
-          vcf=TNseq.TNseq_vcf,
+          vcf=TNseq_fb.TNseq_vcf,
           hg=hg,
           only_pass=only_pass,
           sample_id=sample_id,
@@ -565,17 +557,15 @@ workflow {{ project_name }} {
     }
 
     if (tnscope) {
-      call TNscope.TNscope as TNscope {
+      call TNscope.TNscope as TNscope_fb {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         sample=sample_id,
-        normal_deduped_bam=normal_Dedup.deduped_bam,
-        normal_deduped_bam_index=normal_Dedup.deduped_bam_index,
-        normal_recal_table=normal_BQSR.recal_table,
-        tumor_deduped_bam=tumor_Dedup.deduped_bam,
-        tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
-        tumor_recal_table=tumor_BQSR.recal_table,
+        normal_recaled_bam=normal_BQSR_fb.recaled_bam,
+        normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,
+        tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,
+        tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,
         normal_name=sample_id + "_normal",
         tumor_name=sample_id + "_tumor",
         fasta=fasta,
@@ -591,9 +581,9 @@ workflow {{ project_name }} {
       }
       
       if (annovar) {
-        call ANNOVAR.ANNOVAR as TNscope_annovar {
+        call ANNOVAR.ANNOVAR as TNscope_annovar_fb {
           input:
-          vcf=TNscope.TNscope_vcf,
+          vcf=TNscope_fb.TNscope_vcf,
           hg=hg,
           only_pass=only_pass,
           annovar_database=annovar_database,
@@ -604,9 +594,9 @@ workflow {{ project_name }} {
       }
 
       if (vep) {
-        call VEP.VEP as TNscope_VEP {
+        call VEP.VEP as TNscope_VEP_fb {
           input: 
-          vcf=TNscope.TNscope_vcf,
+          vcf=TNscope_fb.TNscope_vcf,
           hg=hg,
           only_pass=only_pass,
           sample_id=sample_id,
@@ -626,13 +616,13 @@ workflow {{ project_name }} {
     }
 
     if (varscan) {
-      call somatic.somatic as somatic {
+      call somatic.somatic as somatic_fb {
         input:
         sample=sample_id,
-        tumor_bam=tumor_Dedup.deduped_bam,
-        tumor_bam_index=tumor_Dedup.deduped_bam_index,
-        normal_bam=normal_Dedup.deduped_bam,
-        normal_bam_index=normal_Dedup.deduped_bam_index,
+        normal_bam=normal_BQSR_fb.recaled_bam,
+        normal_bam_index=normal_BQSR_fb.recaled_bam_index,
+        tumor_bam=tumor_BQSR_fb.recaled_bam,
+        tumor_bam_index=tumor_BQSR_fb.recaled_bam_index,
         ref_dir=ref_dir,
         fasta=fasta,    
         docker=varscan_docker,
@@ -640,35 +630,35 @@ workflow {{ project_name }} {
         cluster_config=cluster_config
       }
 
-      call processSomatic.processSomatic as processSomatic {
+      call processSomatic.processSomatic as processSomatic_fb {
         input:
         sample=sample_id,
-        varscan_snp=somatic.varscan_snp,
-        varscan_indel=somatic.varscan_indel,   
+        varscan_snp=somatic_fb.varscan_snp,
+        varscan_indel=somatic_fb.varscan_indel,   
         docker=varscan_docker,
         disk_size=disk_size,
         cluster_config=cluster_config
       }
 
-      call somaticFilter.somaticFilter as somaticFilter {
+      call somaticFilter.somaticFilter as somaticFilter_fb {
         input:
         sample=sample_id,
-        varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
-        varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
-        varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
-        varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
-        varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
-        varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
-        varscan_indel=somatic.varscan_indel,   
+        varscan_snp_somatic_hc=processSomatic_fb.varscan_snp_somatic_hc,
+        varscan_snp_germline_hc=processSomatic_fb.varscan_snp_germline_hc,
+        varscan_snp_loh_hc=processSomatic_fb.varscan_snp_loh_hc,
+        varscan_indel_somatic_hc=processSomatic_fb.varscan_indel_somatic_hc,
+        varscan_indel_germline_hc=processSomatic_fb.varscan_indel_germline_hc,
+        varscan_indel_loh_hc=processSomatic_fb.varscan_indel_loh_hc,
+        varscan_indel=somatic_fb.varscan_indel,   
         docker=varscan_docker,
         disk_size=disk_size,
         cluster_config=cluster_config
       }
 
       if (annovar) {
-        call ANNOVAR.ANNOVAR as VarScan_annovar {
+        call ANNOVAR.ANNOVAR as VarScan_annovar_fb {
           input:
-          vcf=somaticFilter.varscan_somatic_filter,
+          vcf=somaticFilter_fb.varscan_somatic_filter,
           hg=hg,
           only_pass=only_pass,
           annovar_database=annovar_database,
@@ -679,9 +669,9 @@ workflow {{ project_name }} {
       }
 
       if (vep) {
-        call VEP.VEP as VarScan_VEP {
+        call VEP.VEP as VarScan_VEP_fb {
           input: 
-          vcf=VarScan.VarScan_vcf,
+          vcf=VarScan_fb.VarScan_vcf,
           hg=hg,
           only_pass=only_pass,
           sample_id=sample_id,