更新 'tasks/hisat2.wdl'

tasks/hisat2.wdl

@@ -9,7 +9,7 @@ task hisat2 {
 
    command {
    	 nt=$(nproc)
-     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam
+     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam --un-conc-gz ${base}_un.fq.gz
    }
    
    runtime { 
@@ -21,5 +21,7 @@ task hisat2 {
 
    output {
       File sam = base + ".sam"
+      File unmapread_1p = base + "_un.fq.1.gz"
+      File unmapread_2p = base + "_un.fq.2.gz"
    }
 }