更新 'tasks/ReadStats.wdl'

tasks/ReadStats.wdl

@@ -4,11 +4,8 @@ task ReadStats {
     File in_log_trimAdatper
     File in_log_readFilter
     File in_log_align_miRNA
-    File in_log_align_preMiRNA
-    File in_log_align_piRNA
-    File in_log_align_tRNA
     File in_log_align_RNA 
-    File in_log_align_hg38
+    File in_log_align_rn7
     File in_sam_align_RNA
 
     String cluster_config
@@ -34,13 +31,11 @@ task ReadStats {
 
         n_miRNA_mature=$(cat ${in_log_align_miRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
         n_miRNA_hairpin=$(cat ${in_log_align_preMiRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
-        n_piRNA=$(cat ${in_log_align_piRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
-        n_tRNA=$(cat ${in_log_align_tRNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
 
         n_RNA=$(cat ${in_log_align_RNA} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
-        n_otGenomic=$(cat ${in_log_align_hg38} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
+        n_otGenomic=$(cat ${in_log_align_rn7} | grep 'at least one reported alignment' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g')
 
-        n_notGenomic=$(cat ${in_log_align_hg38} | grep 'reads that failed to align' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g' )
+        n_notGenomic=$(cat ${in_log_align_rn7} | grep 'reads that failed to align' | head -n 1 | cut -d ':' -f 2 | cut -d '(' -f 1 | sed 's/ //g' )
 
                 
         groupedReadCount=${sample_id}.trimAdapt.filter.align2RNA.grouped.readCount