Removed spaces from workflow file.
Cleaned initialize.sh
Merge branch 'testing' of https://github.com/molgenis/molgenis_apps-legacy
Added and improved tests for compute4. Beware, the tests may be not fully tested and thus they may be incorrect or unfinished.
Switched of R.
Added table to QC-report template.
Moved templates out of protocols folder into template folder of ngsWorkflowRealignmentAndSnpCalling pipeline.
Improvements in argument parsing and validation of inputs. If Header.ftl and Footer.ftl are non-existing then compute will just continue. We should do same for submit.sh.ftl etc..
Moved some templates/protocols
Merge branch 'testing' of https://github.com/molgenis/molgenis_apps-legacy
Removed system templates, because they are stored in template folder
Added table that explains SNP-list in detail (as Appendix 1).
Fixed enabling merge
Merge pull request #430 from mdijkstra/master

My stuff of compute 4 after solving merge conflicts