Introduce mip.pl, decomission mip_align.pl and mip_variation.pl

- MIP is now a single script (mip.pl)
- Improved parameter handling through subroutines
- Improved subroutine for sbatch submission. Can now handle extended forks
- GATK realign and base recalibration is now done on original BAM and not split per chr due to the parallelization option added by GATK
- Cleanup of code and parameters
- IntersectCollect template now dynamically handles fileendings
- changed "-p node" to "-p core" where relevant to accomodate UppMax changes