removed R1 and R2 for option --basename --paired

FelixKrueger · Oct 1, 2019 · 0f631e5 · 0f631e5
1 parent 3617b76
commit 0f631e5
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/trim_galore b/trim_galore
@@ -1323,8 +1323,8 @@ sub trim{
             ### FILE RENAMING
             if ($basename){
                 warn "Now renaming the output files\n\n";
-                my $tempname_1 = "${basename}_R1$1" if ($file_1 =~ /(_trimmed.*)$/);
-                my $tempname_2 = "${basename}_R2$1" if ($file_2 =~ /(_trimmed.*)$/);
+                my $tempname_1 = "${basename}$1" if ($file_1 =~ /(_trimmed.*)$/);
+                my $tempname_2 = "${basename}$1" if ($file_2 =~ /(_trimmed.*)$/);
                 warn "ORIGINAL FILE 1: >>$file_1<<\tRENAMING TO:>>$tempname_1<<\n";
                 warn "ORIGINAL FILE 2: >>$file_2<<\tRENAMING TO:>>$tempname_2<<\n";