input revised

tasks/arcashla.wdl

     command <<<
        mkdir hla_type
        /root/arcasHLA/arcasHLA extract ${bam} -o ${base} --paired -t 8 -v
-       /root/arcasHLA/arcasHLA genotype ${base}.extracted.1.fq.gz ${base}.extracted.2.fq.gz hla_type/${base}.genotype.json
+       /root/arcasHLA/arcasHLA genotype ${base}/${base}.sorted.extracted.1.fq.gz ${base}/${base}.sorted.extracted.2.fq.gz hla_type/${base}.genotype.json
     >>>
 
     runtime {
     }
 
     output {
-      File extracted_1p = base + "extracted.1.fq.gz"
-      File extracted_2p = base + "extracted.2.fq.gz"
+      File extracted_1p = base + ".sorted.extracted.1.fq.gz"
+      File extracted_2p = base + ".sorted.extracted.2.fq.gz"
       Array[File] hla_type = ["hla_type/${base}.genotype.json", "hla_type/${base}.genes.json", "hla_type/${base}.extract.log", "hla_type/${base}.genotype.log"]
     }