上传文件至 'tasks'

tasks/annovar.wdl

@@ -0,0 +1,35 @@
+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"
+  }
+}