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- task annovar {
-
- File varscan_snp
- File varscan_indel
- 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 ${varscan_snp} ${database} -buildver hg38 -out ${sample}_varscan_snp -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 ${varscan_indel} ${database} -buildver hg38 -out ${sample}_varscan_indel -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 $nt
- >>>
-
- runtime {
- docker: docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File avinput_varscan_snp = "${sample}_varscan_snp.avinput"
- File multianno_varscan_snp_txt = "${sample}_varscan_snp.hg38_multianno.txt"
- File multianno_varscan_snp = "${sample}_varscan_snp.hg38_multianno.vcf"
- File avinput_varscan_indel = "${sample}_varscan_indel.avinput"
- File multianno_varscan_indel_txt = "${sample}_varscan_indel.hg38_multianno.txt"
- File multianno_varscan_indel = "${sample}_varscan_indel.hg38_multianno.vcf"
- }
- }
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