test

tasks/annovar.wdl

@@ -20,8 +20,8 @@ task annovar {
       /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
       ${annovar_database} -buildver ${hg} \
       -out ${basename} -remove \
-      -protocol rmsk,exac03,gnomad211_exome,cosmic92_coding,cosmic92_noncoding \
-      -operation r,f,f,f,f \
+      -protocol exac03,gnomad211_exome,cosmic92_coding,cosmic92_noncoding \
+      -operation f,f,f,f \
       -nastring . -vcfinput -thread $nt
     fi
     
@@ -36,7 +36,7 @@ task annovar {
 
   output {
     File avinput = "${basename}.avinput"
-    File rmsk_txt = "${basename}.${hg}_rmsk.txt"
-    File rmsk_vcf = "${basename}.${hg}_rmsk.vcf"
+    File others_txt = "${basename}.${hg}_others.txt"
+    File others_vcf = "${basename}.${hg}_others.vcf"
   }
 }