Added ".bam" ending to index
Added use of dynamic configuration files to facilitate for different users and distribution across clusters
Removed env_up flag
Separated CoverageCalulation into modules, removed pCalculatecoverage, fixed config sampleIDs not being overwritten by pedigree
Moved qc_pedigree.yaml to after infiles
Removed SBATCH '-C thin' feature to facilitate different cluster usage.
Removed last -p node entry
Removed SBATCH '-c thin' from GATK Haplotypecalle from GATK Haplotypecallerr
Removed SBATCH '-c thin ' from correct place this time
Place qc_pedigree at correct position
Added sbatch submission error check, removed jobinfo print since it is specfic to Uppmax, added temp directory clean up for MosaikAlign
Autovivication MosaikAligner, BWA, added new sub routine for file existence check, splitted and rewrote DefineParameters
Bumped version number
Merge branch 'release/v1.4.6'