Fix Bug: input

README.md

@@ -0,0 +1,32 @@
+# README.md
+
+> Author: Yaqing Liu
+> 
+> Email: [yaqing.liu@outlook.com](mailto:yaqing.liu@outlook.com)
+> 
+> Last Updates: 25/04/2021
+
+#### Requirements
+
+- choppy
+- Ali-Cloud
+- Linux
+
+#### Introduction
+Variant calling pipeline from mapping to generating MAF files with three optional callers, i.e. TNseq, TNscope and Varscan2, for WGS and WES data.
+
+**Please carefully check the reference genome, bed file, etc.**
+#### Usage
+```
+open-choppy-env
+
+choppy install YaqingLiu/variant-calling-latest
+
+choppy samples YaqingLiu/variant-calling-latest --no-default
+# sample_id,fastq_1,fastq_2
+
+choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project -l Label
+
+# Query the status of all tasks in the project
+choppy query -L Label | grep "status"
+```

defaults

@@ -7,20 +7,20 @@
     "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",
-    "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
+    "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",
     "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",
+    "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
+    "set_pon": false,
     "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
     "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
     "disk_size": "200",
     "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "germline": "false",
-    "tnseq": "true",
-    "tnscope": "true",
-    "varscan": "true"
+    "germline": false,
+    "tnseq": true,
+    "tnscope": true,
+    "varscan": true
 }

inputs

@@ -18,14 +18,14 @@
   "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.regions": "{{ regions }}",
-  "{{ project_name }}.set_pon": {{ set_pon }},
+  "{{ project_name }}.set_pon": {{ set_pon | tojson }},
   "{{ project_name }}.pon_vcf": "{{ pon_vcf }}",
   "{{ 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 }}.germline": {{ germline }},
-  "{{ project_name }}.tnseq": {{ tnseq }},
-  "{{ project_name }}.tnscope": {{ tnscope }},
-  "{{ project_name }}.varscan": {{ varscan }}
+  "{{ project_name }}.germline": {{ germline | tojson }},
+  "{{ project_name }}.tnseq": {{ tnseq | tojson }},
+  "{{ project_name }}.tnscope": {{ tnscope | tojson }},
+  "{{ project_name }}.varscan": {{ varscan | tojson }}
 }

tasks/TNscope.wdl

@@ -24,7 +24,6 @@ task TNscope {
 	
 	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
 	
-	
 	command <<<
 		set -o pipefail
 		set -e

workflow.wdl

@@ -343,7 +343,7 @@ workflow {{ project_name }} {
 			disk_size=disk_size,
 			cluster_config=cluster_config
 		}
-
+		
 		call annovar.annovar as TNscope_annovar {
 			input:
 			sample=sample_id,