Merge pull request #113 from georgebyelas/master

new gcc workflow
Merge pull request #114 from georgebyelas/master

fixed parameters file
Merge pull request #115 from georgebyelas/master

5gpm pipeline for gcc cluster settings
Merge pull request #116 from georgebyelas/master

added parameters file to 5gpm
Merge pull request #117 from georgebyelas/master

added new step + few corrections
RNA-seq
Merge pull request #118 from PatrickDeelen/master

RNA-seq
Added RNA-seq genotype calling with GATK and Beagle imputation pipelines
Merge pull request #119 from DashaZhernakova/master

Added RNA-seq genotype calling with GATK and Beagle imputation pipelines
small fixes
Merge pull request #120 from DashaZhernakova/master

small changes in Beagle pipeline
added multithreading in Beagle
Merge pull request #121 from DashaZhernakova/master

added multithreading in Beagle
Merge pull request #122 from georgebyelas/master

fixed parameter file
Merge pull request #123 from georgebyelas/master

removed R_HOME, which does not work from 2 workflows
changed realignment protocol from 1 to 4 cores
Merge pull request #124 from RoanKanninga/master

changed realignment protocol from 1 to 4 cores
updated the parameters file
put the tmpIntermediateDir back
Merge pull request #125 from RoanKanninga/master

updated the parameters file