id,summary,reporter,owner,description,type,status,priority,milestone,component,resolution,keywords,cc 614,Improve error handling when executing jobs on the cluster,Nicklas Nordborg,Nicklas Nordborg,"Error handling is important for the functionality of the Reggie<->Cluster integration. In the ideal world all scripts should work as expected and produce some results, and when they don't a sensible error message should be given and made visible through the Reggie/BASE interface. The cluster wrapper currently assumes that scripts that are successful return exit code=0 and scripts that fail return exit code != 0. If the script fails the contents of the 'stderr' stream is used as the error message. Unfortunately not all scripts/programs we use follows this pattern. The first step is to investigate the programs and see if we can make them behave more like we want. The (possible incomplete) list of programs: * picard * trimmomatic * bowtie2 * tophat * samtools * the pipeline scripts ",task,closed,major,Reggie v2.16,net.sf.basedb.reggie,fixed,,