task-hla-revised

tasks/arcashla.wdl

     command <<<
        mkdir hla_type
        /root/arcasHLA/arcasHLA extract ${bam} -o ${base} --paired -t 8 -v
-       /root/arcasHLA/arcasHLA genotype ${base}/${base}.sorted.extracted.1.fq.gz ${base}/${base}.sorted.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o hla_type/${base}.genotype.json -t 8 -v
+       /root/arcasHLA/arcasHLA genotype ${base}/${base}.sorted.extracted.1.fq.gz ${base}/${base}.sorted.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o hla_type -t 8 -v
     >>>
 
     runtime {