input revised

tasks/arcashla.wdl

@@ -6,7 +6,7 @@ task arcashla {
 
     command <<<
        mkdir hla_type
-       /root/arcasHLA/arcasHLA extract ${bam} -o ${base}.extracted.fq.gz --paired -t 8 -v
+       /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
     >>>