NIPT-v3.0.2

Fixed bugs:

• Missing version number for "module load" commands.
• Missing "module list" commands.
• To low wrong amount of mem requested for Run protocol.
• Changed protocol to compensate for changed folder structure for data from Utrecht.

NGS_Automated 1.0.7

bugfixes + upgrade to NGS_DNA-3.2.5

New releases can be found in https://github.com/molgenis/NGS_Automated/releases

NGS_Automated 1.0.6

upgrade to NGS_DNA-3.2.4 + bugfixes

NGS_Automated 1.0.5

fix issue that dataCopiedToPrm file is not created

NGS_Automated 1.0.4

• make logs directory more structured
• renamed copyRawDataToZinc to CopyRawDataToDiagnosticsCluster

NGS_Automated 1.0.3

• fixing exclude path in rsync
• removing unnecessary and not possible chmod

NGS_Automated 1.0.2

• added extra copy of the samplesheet to prm (now also to rawdata/ngs dir)
• removed unused code
• fixing excluded path in copyprojectdataToResultsDir

NGS_Automated 1.0.1

• updated the versioning, it is not independent now (not the same version as the NGS_DNA and NGS_RNA pipelines)

NGS_RNA-3.2.3 (Frog)

• update to Molgenis Compute Molgenis-Compute-v16.05.1, with preperations for automatic start of pipelines
• Added more documetation
• The following bugfixes:

*MergeBam step contains symlink with absolute path bug enhancement NGS_RNA #497
*There is no insertsize metrics when SR bug NGS_RNA #496
*Kallisto is not working, missing index file bug NGS_RNA #490
*Add strandedness-option: yes | no | reverse for HT-seq count bug enhancement NGS_RNA #446

NGS_DNA-3.2.2 pipeline (Caribou)

• Changed CoveragePerBase protocol into CoverageCalculations
• Added Coverage calculations for subset bed files (LEVER, NEURO, SSID and GEO)
• Changed output for coverage per target and coverage per base
• CoveragePerBase added missing make genesOnly file + VariantCalling bug (double brackets)
• increased memory for MarkDuplicates
• improved the copy prmtotmp data (when prm is not available on zinc-finger it will download it from calculon)
• bugfix in CheckIlluminaEncoding (where '++' is not used anymore, it is now '+1')
• added automating:
  • start of pipeline
  • copying to prm
  • copying to zinc-finger
• fixed the duplication rate in the QC report
• Made new QCReport (in html)
• bugfix #439 fixing the GenderCalculate
• bugfix #457 fixing CheckIlluminaEncoding
• bugfix #463
• fix issue with samples on multiple lanes and counting number of samples in generate.sh