update dowload components to properly clos filehandlers. Update CASAVANG6WF class to add a funtion that will run all casava specific process (illumina filter, demultiplexstat etc...) This makes the code cleaner for all casavang6workflows. This class has also been updated to be able to use --sample option.

Remove --casava-project parameter from CasavaNG6Workflow, it is retrieved from samplesheet
Update fastqc component to take new metrics

fix subsetAssignation analysis. casava parameters are not part of a parameterlist anymore. update all casava test config files

Fix demultiplexstat analysis for indexes with mismatch. Fix casavaNG6Workflows, now undetermined reads are retrieved correcctly

The gene diversity worflow and associated components are updated to new jflow version.
The phiX workflow is also updated