Added beagle and minimac pipelines
corrected mixed content in mach_minimach workflow
Added Create Batches for ImputationTool
added batches to workflow
added studyTriTyperBatchChrDir in parameters
createbatches is after convertPedMaptoTrityper
Added prepareStudyWithBatches.ftl
Merge branch 'master' of github.com:kantale/molgenis_apps
study preparation is done with batches
Update modules/compute/protocols/imputation/beagle/prepareStudyWithBatches.ftl

Altered from preparedStudy so that it includes batches
Update modules/compute/protocols/imputation/beagle/prepareStudyWithBatches.ftl

Syncing with parameters from impute2 
typo: Forgot \ in end of command
added batches.txt at the command line
Reference location (gonl_release3.1) was renamed
add batches
added batches to the example
Add batches to imputation beagle command
typo: beagle instead of batch
Added --rs option (to match correctly the SNP ids)
Remove "Status" from .snps file