|
- task annovar {
-
- File tnscope_vcf_file
- File tnseq_vcf_file
- File database
- String sample
- String docker
- String cluster_config
- String disk_size
-
-
- command <<<
- set -o pipefail
- set -e
- nt=$(nproc)
- /installations/annovar/table_annovar.pl ${tnscope_vcf_file} ${database} -buildver hg19 -out ${sample}_tnscope -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20170130,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
- /installations/annovar/table_annovar.pl ${tnseq_vcf_file} ${database} -buildver hg19 -out ${sample}_tnseq -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20170130,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
- >>>
-
- runtime {
- docker: docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File avinput_tnscope = "${sample}_tnscope.avinput"
- File multianno_tnscope_txt = "${sample}_tnscope.hg19_multianno.txt"
- File multianno_tnscope_vcf = "${sample}_tnscope.hg19_multianno.vcf"
- File avinput_tnseq = "${sample}_tnseq.avinput"
- File multianno_tnseq_txt = "${sample}_tnseq.hg19_multianno.txt"
- File multianno_tnseq_vcf = "${sample}_tnseq.hg19_multianno.vcf"
- }
- }
|
