Dirk's first commit
changed some protocols (deleted unused tmpfolders), added complete protocols: IndelMerge,MergeChrAndSplitVariants,MergeIndelCalls,Pindel. SnpEff protocols is WIP
Merge pull request #141 from RoanKanninga/master

changed some protocols (deleted unused tmpfolders), added complete proto...
first protocols for RNA pipeline
Merge pull request #142 from Gerbenvandervries/master

first protocols for RNA pipeline
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines

Regular merge with blessed master.
Functioning pipeline version 0.1 for utrecht data (.bam files).
Merge pull request #143 from dirkdeweerd/master

Functioning pipeline version 0.1 for utrecht data (.bam files).
added fastqc and copy results protocols
Merge pull request #144 from Gerbenvandervries/master

added fastqc and copy results protocols
fixed paste tab problem
Merge pull request #145 from kantale/master

fixed paste tab problem
New parameter file for NIPT pipeline specified for the 5GPM paths and software
Merge pull request #146 from ljohansson/master

New parameter file for NIPT pipeline specified for the 5GPM paths and so...
added QCstat protocol, and added parameter and workflow for that step
Merge pull request #147 from Gerbenvandervries/master

added QCstat protocol, and added parameter and workflow for that step
added protocol for genereating a qc report
Merge pull request #148 from Gerbenvandervries/master

added protocol for genereating a qc report
added .gitignore and .classpath to gitignopre file
Added new parameterfile and workflow file and added script for copying results files to resultsdir after running the pipeline is completed