input revised

tasks/arcashla.wdl

     }
 
     output {
-      File extracted_1p = base + ".sorted.extracted.1.fq.gz"
-      File extracted_2p = base + ".sorted.extracted.2.fq.gz"
+      File extracted_1p = "${base}/${base}.sorted.extracted.1.fq.gz"
+      File extracted_2p = "${base}/${base}.sorted.extracted.2.fq.gz"
       Array[File] hla_type = ["hla_type/${base}.genotype.json", "hla_type/${base}.genes.json", "hla_type/${base}.genotype.log"]
     }