id,summary,reporter,owner,description,type,status,priority,milestone,component,resolution,keywords,cc 743,The second trimmomatic step in demux script may not include options,Nicklas Nordborg,Nicklas Nordborg,"When generating the script for the second trimmomatic step the options specified may not be included since there is an incorrect check: {{{ if (demux_trimmomaticOptions1 != null) { trimCmd2 += "" "" + demux_trimmomaticOptions2; } }}} The `if` statement should check `demux_trimmomaticOptions2`. Fortunately both options are required and should never be null at this stage.",defect,closed,trivial,Reggie v3.2,net.sf.basedb.reggie,fixed,,