Change over from wiggle files to bedgraph files to profile reads. Reasons are

[htsworkflow.git] / htswanalysis / scripts / ConfigureTasks.pm

diff --git a/htswanalysis/scripts/ConfigureTasks.pm b/htswanalysis/scripts/ConfigureTasks.pm
index d4348c8b25b10273ac9a0141740909de24d384ea..183d0607ac762d3aa9968ffd2ece8bfd495384fc 100755 (executable)
--- a/htswanalysis/scripts/ConfigureTasks.pm
+++ b/htswanalysis/scripts/ConfigureTasks.pm
@@ -235,7 +235,7 @@ sub WriteProfileTasks {
 
       my $seqcheck = "if [ ! -e $data_dir/Libraries/$lib.txt ]; then $root_dir/scripts/analys_track_main.py updsts $task \"Waiting for sequencing.\"; fi;"; 
       my $cmds .= "$lib.wig.gz: $data_dir/Libraries/$lib.txt\n";
-      $cmds .= "\t".$PROFILEDIR.'/profile_reads_wig '.$data_dir.'/Libraries/'.$lib.'.txt "'.$name.'" "'.$name.'" | gzip > '.$lib.'.wig.gz';
+      $cmds .= "\t".$PROFILEDIR.'/profile_reads_bedgraph '.$data_dir.'/Libraries/'.$lib.'.txt "'.$name.'" "'.$name.'" | grep -v contam | grep -v Ribo | grep -v splice | gzip > '.$lib.'.wig.gz';
       $cmds .= "\n\n";
       $cmds .= $lib.'.profile.gif: '.$data_dir.'/Libraries/'.$lib.'.txt '.$root_dir.'/reference_data/'.$genome.'_tx_start_sites'."\n";
       $cmds .= "\t".$PROFILEDIR.'/profile_reads_against_features $^ | '.$root_dir.'/scripts/profile_to_svg.pm | /opt/local/bin/convert - $@'."\n";