Merge pull request #28 from ljohansson/master

added templates parameter to CreateInHouseProjects.ftl
Updated walltime in parameters
Updates on in-house pipeline. Fixed bug in indel merging, now uses fasta index as input to sort output on.
Improved permission and error handling in the NGS_de_novo_assembly workflow.
Merge pull request #29 from freerkvandijk/master

Updated walltimes in impute2 pipeline and fixed small bug of missing Fasta index file for InDel calling in the alignment and variant calling pipeline
Merge pull request #30 from pneerincx/master

NGS_de_novo_assembly workflow improvements
Moved step to create per sample final report files (with array data) to new GAF workflow and removed outdated NGS_data_archiving workflow.
compute4/NGS_de_novo_assembly/protocols/Abyss.ftl
Fixed listing of FastQ input files per library when there is only one.
Merge pull request #31 from pneerincx/master

Updated GAF workflow to create array final reports per sample.
Bug fix in VCF to table protocol
Added paramter for the latest dbSNP version.
Merge pull request #33 from pneerincx/master

Added parameter for the latest dbSNP version.
Fixed bugs in GAF/Bcl2Fastq workflow: added missing params for CreateFinalReport step and improved handling of tmp dirs to make it compatible with both local execution as well as running on a cluster node.
Merge pull request #34 from pneerincx/master

Fixed bugs in GAF/Bcl2Fastq workflow.
fixed conflict in merge
Improvements to creation of final reports per sample.
Fixed lot's of typos related to different env on new server.
Merge pull request #35 from pneerincx/master

Small fixes for the GAF data archiving workflow.
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines