docker

codescripts/voted_by_vcfinfo_mendelianinfo.py

@@ -80,10 +80,10 @@ benchmark_LCL8 = open('LCL8_voted.vcf','w')
 all_sample_outfile = open('all_sample_information.txt','w')
 
 # write VCF
-LCL5_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t LCL5_benchmark_calls\n'
-LCL6_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t LCL6_benchmark_calls\n'
-LCL7_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t LCL7_benchmark_calls\n'
-LCL8_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t LCL8_benchmark_calls\n'
+LCL5_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5_benchmark_calls\n'
+LCL6_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL6_benchmark_calls\n'
+LCL7_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL7_benchmark_calls\n'
+LCL8_col = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL8_benchmark_calls\n'
 
 benchmark_LCL5.write(vcf_header)
 benchmark_LCL5.write(LCL5_col)
@@ -214,7 +214,7 @@ def consensus_call(vcf_info_list,mendelian_list,alt_seq):
 	elif ((pcr_consensus != './.') or (pcr_consensus not in tag)) and ((pcr_free_consensus in tag) and (pcr_free_consensus == './.')):
 		consensus_call = 'pcr-speicifc'			
 	elif (pcr_consensus == '0/0') and (pcr_free_consensus == '0/0'):
-		consensus_call = 'confirm for parents'								
+		consensus_call = '0/0'								
 	else:
 		consensus_call = 'filtered'
 	return pcr_consensus, pcr_free_consensus, mendelian_num, consensus_call, consensus_alt_seq, ALL_ALT, ALL_DP, detected_num

inputs

@@ -1,12 +1,12 @@
 {
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
-  "{{ project_name }}.two_family_merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.2",
+  "{{ project_name }}.two_family_merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.3",
   "{{ project_name }}.LCL6mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "{{ project_name }}.LCL5mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "{{ project_name }}.disk_size": "150",
   "{{ project_name }}.chromo": "{{ chromo }}",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ project_name }}.votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.2",
+  "{{ project_name }}.votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.3",
   "{{ project_name }}.cluster_config": "OnDemand bcs.b4.xlarge img-ubuntu-vpc",
   "{{ project_name }}.vcf": "{{ vcf }}",
   "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"

tasks/votes.wdl

@@ -17,10 +17,10 @@ task votes {
 
 		python /opt/voted_by_vcfinfo_mendelianinfo.py -folder ./temp -vcf vcf_info.txt
 
-		cp LCL5_voted.vcf LCL5.$chromo}voted.vcf
-		cp LCL6_voted.vcf LCL6.$chromo}voted.vcf
-		cp LCL7_voted.vcf LCL7.$chromo}voted.vcf
-		cp LCL8_voted.vcf LCL8.$chromo}voted.vcf
+		cp LCL5_voted.vcf LCL5.${chromo}.voted.vcf
+		cp LCL6_voted.vcf LCL6.${chromo}.voted.vcf
+		cp LCL7_voted.vcf LCL7.${chromo}.voted.vcf
+		cp LCL8_voted.vcf LCL8.${chromo}.voted.vcf
 
 	>>>
 
@@ -31,10 +31,10 @@ task votes {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File LCL5_voted_vcf = "LCL5.$chromo}voted.vcf"
-		File LCL6_voted_vcf = "LCL6.$chromo}voted.vcf"
-		File LCL7_voted_vcf = "LCL7.$chromo}voted.vcf"
-		File LCL8_voted_vcf = "LCL8.$chromo}voted.vcf"
+		File LCL5_voted_vcf = "LCL5.${chromo}.voted.vcf"
+		File LCL6_voted_vcf = "LCL6.${chromo}.voted.vcf"
+		File LCL7_voted_vcf = "LCL7.${chromo}.voted.vcf"
+		File LCL8_voted_vcf = "LCL8.${chromo}.voted.vcf"
 		File all_sample_info = "all_sample_information.txt"
 	}
 }