update input

defaults

   "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
   "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
-  "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
-  "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
-  "maftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
-  "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
-  "database": "oss://pgx-reference-data/annovar_hg38/",
-  "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
-  "set_pon": "true",
-  "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
-  "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
+  "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Padded.bed",
   "disk_size": "200",
-  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-  "set_annovar": "true",
-  "set_vcf2maf": "true",
-  "germline": "false"
+  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"
 }

inputs

 {
   "{{ project_name }}.panel_id": "{{ panel_id }}",
-  "{{ project_name }}.normal_recaled_bam_bai": {{ normal_recaled_bam_bai | tojson }},
+  "{{ project_name }}.deduped_bam": "{{ deduped_bam }}",
+  "{{ project_name }}.deduped_bam_index": "{{ deduped_bam_index }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
   "{{ project_name }}.dbsnp": "{{ dbsnp }}",
   "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
   "{{ project_name }}.db_mills": "{{ db_mills }}",
   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
-  "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
-  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
-  "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
-  "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.regions": "{{ regions }}",
-  "{{ project_name }}.set_pon": {{ set_pon }},
-  "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
-  "{{ project_name }}.cosmic_dir": "{{ cosmic_dir }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
-  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
-  "{{ project_name }}.set_annovar": {{ set_annovar }},
-  "{{ project_name }}.set_vcf2maf": {{ set_vcf2maf }},
-  "{{ project_name }}.germline": {{ germline }}
-}
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/BQSR.wdl

   
   File ref_dir
   File dbsnp_dir
+  String dbsnp
   File dbmills_dir
+  String db_mills
   
   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

tasks/PoN.wdl

   String SENTIEON_LICENSE
   File ref_dir
   String fasta
-  File cosmic_dir
-  String cosmic_vcf
-  File dbsnp_dir
-  String dbsnp
   File regions
 
   File normal_bam
     set -e
     export SENTIEON_LICENSE=${SENTIEON_LICENSE}
     nt=$(nproc)
-    mkdir -p /cromwell_root/tmp/cosmic/
-    cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
 
-    # Generating TNhaplotyper PoN
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_TNhaplotyper_pon.vcf
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
 
-    # Generating TNhaplotyper2 PoN
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper2 --normal_sample ${sample} ${sample}_TNhaplotyper2_pon.vcf
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt $INTERVAL -r ${ref_dir}/${fasta} -i ${normal_bam} \
+    --algo TNhaplotyper2 --normal_sample ${sample} ${sample}.TNseq.PoN.vcf
 
-    # Generating TNscope PoN
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNscope --normal_sample ${sample} ${sample}_TNscope_pon.vcf
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt $INTERVAL -r ${ref_dir}/${fasta} -i ${normal_bam} \
+    --algo TNscope --normal_sample ${sample} ${sample}.TNscope.PoN.vcf
   >>>
   
   runtime {
   }
 
   output {
-    File TNhaplotyper_pon_vcf = "${sample}_TNhaplotyper_pon.vcf"
-    File TNhaplotyper2_pon_vcf = "${sample}_TNhaplotyper2_pon.vcf"
-    File TNscope_pon_vcf = "${sample}_TNscope_pon.vcf"
+    File TNseq_pon_vcf = "${sample}.TNseq.PoN.vcf"
+    File TNscope_pon_vcf = "${sample}.TNscope.PoN.vcf"
   }
 }

tasks/Realigner.wdl

   output {
     File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
     File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
-
   }
 }
 

workflow.wdl

   String SENTIEON_LICENSE
   String panel_id
 
+  File deduped_bam
+  File deduped_bam_index
+  File regions
   File ref_dir
   String fasta
-  File cosmic_dir
-  String cosmic_vcf
   File dbsnp_dir
   String dbsnp
-  File regions
+  File dbmills_dir
+  String db_mills
 
-  Array[Array[File]] normal_recaled_bam_bai
   String sentieon_docker
   String cluster_config
   String disk_size
     SENTIEON_LICENSE=SENTIEON_LICENSE,
     fasta=fasta,
     ref_dir=ref_dir,
-    deduped_bam=Dedup.deduped_bam,
-    deduped_bam_index=Dedup.deduped_bam_index,
+    deduped_bam=deduped_bam,
+    deduped_bam_index=deduped_bam_index,
     db_mills=db_mills,
     dbmills_dir=dbmills_dir,
     sample=sample_id + '_tumor',
     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