添加 'tasks/AnnotSV.wdl'

tasks/AnnotSV.wdl

@@ -0,0 +1,36 @@
+task AnnotSV {
+  
+  String sample
+  File somatic_vcf
+  File? germline_vcf
+  File annotsv_database
+  String docker
+  String cluster_config
+  String disk_size
+  
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    export ANNOTSV=/opt/AnnotSV
+    if [ ${somatic_vcf} ]; then
+      $ANNOTSV/bin/AnnotSV -SVinputFile ${somatic_vcf} -outputFile ${sample}.somatic.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database} -outputDir .
+    fi
+    if [ ${germline_vcf} ]; then
+      $ANNOTSV/bin/AnnotSV -SVinputFile ${germline_vcf} -outputFile ${sample}.germline.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database} -outputDir .
+    fi
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File AnnotSV_somatic_SV = "${sample}.somatic.SV.annotated.tsv"
+    File? AnnotSV_germline_SV = "${sample}.germline.SV.annotated.tsv"
+  }
+}