删除 'tasks/AnnotSV.wdl'

tasks/AnnotSV.wdl

@@ -1,36 +0,0 @@
-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"
-  }
-}