Merge pull request #131 from pneerincx/master

Updated 5GPM pipeline
deleted a typo, hopefully this will fix the VariantCalling
Merge pull request #132 from RoanKanninga/master

deleted a typo, hopefully this will fix the VariantCalling
fixed fq.gz.md5 links + fix for when Barcode == None
Merge pull request #133 from RoanKanninga/master

fixed fq.gz.md5 links + fix for when Barcode == None
fixed the multiple projects issue, the wrong worksheet was used
Merge pull request #134 from RoanKanninga/master

fixed the multiple projects issue, the wrong worksheet was used
loading R/2.14.2 version for GATK/1.2-1-g33967a4 UnifiedGenotyper
Merge pull request #135 from Gerbenvandervries/master

loading R/2.14.2 version for GATK/1.2-1-g33967a4 UnifiedGenotyper
changed protocols, edited parameter tmpvariables to tmpfolders/files created by a function in the header
removed unused tmp folders
removed fi
Merge pull request #136 from RoanKanninga/master

changed protocols, edited parameter tmpvariables to tmpfolders/files cre...
changed a parameter
Merge pull request #137 from RoanKanninga/master

changed a parameter
new Chromosome merge, and variantspit protocol
parameterfile added for all exon and cgd targets analysis
Revert "new Chromosome merge, and variantspit protocol"

This reverts commit 7faf8a01027e47696d21dabe22f6cdd444326807.
Merge pull request #138 from Gerbenvandervries/master

parameter file added for merged all exon and CGD targets for 5GPM_gcc pipeline
removed the 'old' .fq.gz.md5 extension (changed it into fq.md5)