fix(AnnotSV): output dir

tasks/AnnotSV.wdl

@@ -15,9 +15,10 @@ task AnnotSV {
     
     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}
-    else
-      $ANNOTSV/bin/AnnotSV -SVinputFile ${germline_vcf} -outputFile ${sample}.germline.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database}
+      $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
   >>>