Merge pull request #41 from freerkvandijk/master

Quick concordance check pipeline
missing [sample_index] on line 47 in CreateInhouseProjects.ftl for SR demultiplexedSampleFastqChecksumFilenameSR inserted
Merge pull request #42 from ljohansson/master

added missing [sample_index]  at demultiplexedSampleFastqChecksumFilenameSR in CreateInhouseProjects.ftl
Changed path to workflowfil from 'workflowFile,${McDir}/workflow/in-house_workflow_realignmentAndSnpCalling.csv' to 'workflowFile,${McDir}/pipelines/production/NGS_alignment_SNP_calling/in-house_workflow_realignmentAndSnpCalling.csv' because of the changed location of this files in the pipeline move to molgenis-pipelines
Merge pull request #43 from ljohansson/master

changed location of workflowFile in in-house_parameters_gpfs.csv
Changed protocol for SingleRead. Symlink to rawdata/FastQ file was not correct.
Merge pull request #44 from Gerbenvandervries/master

Change in CreateInhouseProjects.ftl
Added CreateCoverageBedFile protocol to in-house pipeline