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- task annovar {
-
- File TNscope_vcf
- File TNseq_vcf
- 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} ${database} -buildver hg38 -out ${sample}.TNscope -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
- /installations/annovar/table_annovar.pl ${TNseq_vcf} ${database} -buildver hg38 -out ${sample}.TNseq -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,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 = "${sample}.TNscope.hg38_multianno.txt"
- File multianno_TNscope_vcf = "${sample}.TNscope.hg38_multianno.vcf"
- File avinput_TNseq = "${sample}.TNseq.avinput"
- File multianno_TNseq_txt = "${sample}.TNseq.hg38_multianno.txt"
- File multianno_TNseq_vcf = "${sample}.TNseq.hg38_multianno.vcf"
- }
- }
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