id,summary,reporter,owner,description,type,status,priority,milestone,component,resolution,keywords,cc 834,Auto-analyze when sequencing has ended,Nicklas Nordborg,Nicklas Nordborg,"Reggie should be able to automatically detect when a sequencing run has ended and, after making some checks, start the demux step and other downstream secondary analysis. The ""Register sequencing started"" wizard should have an option to enable the automatic analysis. It should be something that is similar to the ""auto-confirm"" option in the ""Start demux"" wizard. Implementation details: * When the auto-analyze option is enabled the `SequencingRun` item is connected with a `Job` (external). * A signal handler is used for status updates. We need to implement a new handler that is similar to the Open Grid Scheduler handler. * The signal handler will check the `` for certain files and update the job status based on which files that are present: - no files found --> WAITING - Data folder found --> EXECUTING (clustering) - `RunParameters.xml` --> EXECUTING (sequencing) - `RunCompletionStatus.xml` --> DONE - (more investigations may be needed) * When the sequencing has completed it should import data from the files just as if the ""Register sequencing ended"" wizard had been used. * It should always be possible to run the ""Register sequencing ended"" wizard manually. * The auto-confirmation service will then take over and detect the ended job. It should run either `picard` or the `genseq_check_illumina_dir.pl` program for a preliminary check. * If all seems to be ok, the demux step should be started using the default options (including auto-confirm=true). ",task,closed,critical,Reggie v4.1,net.sf.basedb.reggie,fixed,,