更新 'tasks/hisat2.wdl'

tasks/hisat2.wdl

@@ -17,7 +17,19 @@ task hisat2 {
    
    command <<<
       nt=$(nproc)
-      hisat2 -t -p $nt -x ${idx}/${idx_prefix} --pen-cansplice ${pen_cansplice} --pen-noncansplice ${pen_noncansplice} --pen-intronlen ${pen_intronlen} --min-intronlen ${min_intronlen} --max-intronlen ${max_intronlen} --maxins ${maxins} --minins ${minins} --rna-strandness RF --un-conc-gz ${sample_id}_un.fq.gz -1 ${Trim_R1} -2 ${Trim_R2} -S ${sample_id}.sam 
+      hisat2 -t -p $nt \
+                -x ${idx}/${idx_prefix} \
+                --pen-cansplice ${pen_cansplice} \
+                --pen-noncansplice ${pen_noncansplice} \
+                --pen-canintronlen ${pen_intronlen} \
+                --min-intronlen ${min_intronlen} \
+                --max-intronlen ${max_intronlen} \
+                --maxins ${maxins} --minins ${minins} \
+                --rna-strandness RF \
+                --un-conc-gz ${sample_id}_un.fq.gz \
+                -1 ${Trim_R1} \
+                -2 ${Trim_R2} \
+                -S ${sample_id}.sam 
    >>>
    
    runtime {