Update: inputs

defaults

@@ -9,13 +9,14 @@
   "SENTIEON_LICENSE": "192.168.0.55:8990",
   "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+  "database": "oss://pgx-reference-data/annovar_hg38/",
   "germline_resource": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
   "germline_resource_tbi": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
+  "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
+  "interval_padding": "10",
   "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
   "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3",
   "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
-  "database": "oss://pgx-reference-data/annovar_hg38/",
-  "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
   "tnseq_pon": "",
   "tnscope_pon": "",
   "disk_size": "200",

inputs

@@ -4,21 +4,22 @@
   "{{ project_name }}.tumor_fastq_2": "{{ tumor_fastq_2 }}",
   "{{ project_name }}.normal_fastq_1": "{{ normal_fastq_1 }}",
   "{{ project_name }}.normal_fastq_2": "{{ normal_fastq_2 }}",
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
+  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
+  "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
+  "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
+  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
   "{{ project_name }}.dbsnp": "{{ dbsnp }}",
   "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
-  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
-  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
   "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
   "{{ project_name }}.db_mills": "{{ db_mills }}",
   "{{ project_name }}.germline_resource": "{{ germline_resource }}",
   "{{ project_name }}.germline_resource_tbi": "{{ germline_resource_tbi }}",
-  "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
-  "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
-  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
-  "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.interval_padding": "{{ interval_padding }}",
+  "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.tnseq_pon": "{{ tnseq_pon }}",
   "{{ project_name }}.tnscope_pon": "{{ tnscope_pon }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
@@ -27,4 +28,4 @@
   "{{ project_name }}.tnseq": {{ tnseq | tojson }},
   "{{ project_name }}.tnscope": {{ tnscope | tojson }},
   "{{ project_name }}.varscan": {{ varscan | tojson }}
-}
+}

tasks/TNscope.wdl

@@ -42,7 +42,7 @@ task TNscope {
     else
       PON=""
     fi
-    
+
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} $INTERVAL \
     -i ${tumor_recaled_bam} -q ${tumor_recal_table} \
@@ -65,5 +65,4 @@ task TNscope {
     File TNscope_vcf= "${sample}.TNscope.TN.vcf"
     File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
   }
-
 }

tasks/TNseq.wdl

@@ -84,5 +84,4 @@ task TNseq {
     File contamination_segments = "${sample}.contamination.segments"
     File orientation = "${sample}.orientation"
   }
-
 }

tasks/somatic.wdl

@@ -22,9 +22,10 @@ task somatic {
     systemDisk: "cloud_ssd 40"
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
+  
   output {
     File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
     File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
     
   }
-}
+}

workflow.wdl

@@ -37,23 +37,22 @@ workflow {{ project_name }} {
   String dbsnp
   File germline_resource
   File germline_resource_tbi
+  File database
   
   File? regions
   Int? interval_padding
-
-  File database
-  String disk_size
-  String cluster_config
-
   File? tnseq_pon
   File? tnscope_pon
 
+  String disk_size
+  String cluster_config
+  
   Boolean haplotyper
   Boolean tnseq
   Boolean tnscope
   Boolean varscan
 
-  if (tumor_fastq_1 != "") {
+  if ( tumor_fastq_1 != "" ) {
     call mapping.mapping as tumor_mapping {
       input: 
       group=sample_id + '_tumor',