删除 'tasks/ANNOVAR.wdl'

tasks/ANNOVAR.wdl

@@ -1,35 +0,0 @@
-task ANNOVAR {
-
-  File vcf
-  String basename = basename(vcf,".vcf")
-  File annovar_database
-  String docker
-  String cluster_config
-  String disk_size
-
-  command <<<
-    set -o pipefail
-    set -e
-    nt=$(nproc)
-    
-    /installations/annovar/table_annovar.pl ${vcf} \
-    ${annovar_database} -buildver hg38 \
-    -out ${basename} -remove \
-    -protocol refGene,cytoBand,genomicSuperDups,clinvar_20220320,intervar_20180118,cosmic95_coding,cosmic95_noncoding,gnomad211_exome,dbnsfp42c,avsnp150 \
-    -operation g,r,r,f,f,f,f,f,f,f \
-    -nastring . -vcfinput -polish -thread $nt
-  >>>
-  
-  runtime {
-    docker: docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-  }
-  
-  output {
-    File avinput = "${basename}.avinput"
-    File multianno_txt = "${basename}.hg38_multianno.txt"
-    File multianno_vcf = "${basename}.hg38_multianno.vcf"
-  }
-}