Only log debug level if specified in the config
Removing default logging of DEBUG level, started moving more things to logger2 (logbook) rather than logger.
Moved most logging to logbook, made print to log
Merge in changes from updatream. Integrate logging and the progress recording
Processing progress logging to show progress step, sendign exceptions over the logbook logger
Started on a log message router added to scripts as bcbb_log_subscriber.py
Made the log subscriber script (bcbb_log_subscriber) more user friendly
Merge from upstream
Cleaned up some. Apparantly something is breaking the RabbitMQ connection in the
variantcalling step
indicator file for successful fastq conversion
changed pipeline progress logs to use utc timestamp
add hooks for processing
refactored illumina_finished_msg.py
added option to write gzip output in qseq to fastq conversion
added processing of undetermined indices
method for calling extract_barcodes
added logging of casava output
parse --ignore-missing-... from config
more specific regexp for getting flowcell directories
test _get_directories() and bugfix