Merge pull request #10 from pneerincx/master

Added new GAF and de-novo assembly workflows + updated gitignore.
Changes to impute2 pipeline, put/getFile added.
added empty (worksheet) parameters for db version
Merge branch 'master' of github.com:molgenis/molgenis-pipelines
Small modification in impute2Imputation.ftl
Merge pull request #11 from freerkvandijk/master

Bugfix in impute2 protocol
Fixed bug in impute2Imputation.ftl
Merge pull request #12 from freerkvandijk/master

Bugfix in impute2Imputation.ftl
Fixed bug in impute2 pipeline. Added first version of shapeIt phasing pipeline.
Merge pull request #13 from freerkvandijk/master

Fixed bug in imputation pipeline, added first version of phasing pipeline.
Test worksheet
Merge pull request #14 from PatrickDeelen/master

test worksheet impute2
Updated impute2 imputation step

Diverse improvements of bash scripts
Added some missing inputs
Default on repro back to PBS
Updated impute2 merge step

Fixed bash array handeling
Bug fix impute2
Merge pull request #15 from PatrickDeelen/master

Impute2 updates
Added impute2 file option
Update readme
Merge pull request #16 from PatrickDeelen/master

Impute2 update and readme update