Demultiplexing pipeline 2.1.2

• fix bug in writing .finished file to correct logs directory
• fixing cronjob
• added copying data to molgenis06

NGS_RNA-3.2.2 (Frog)

• Variant calling per chromosome
• bugfixes for qc statistics per sample in qc report
• readme text updated
• automated detection of strandedness based on prepKit

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NGS_RNA-3.2.1 (elephant)

added:

• more flexibility between genome build
• more flexibility for running the pipeline on different animals
• added pipeline version to QC report
• added tool versions to the genarated README
• bugfix for Flagstat and Hisat statistics in QC report

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Demultiplexing pipeline 2.1.1

• small fix in moving data to results dir (before: everything from intermediateDir was moved into results dir, now only sample specific results)

NGS_DNA-3.2.1 pipeline (Caribou)

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Major changes:

• Replaced Picard tools SortBam, MergeBam and MarkDuplicates for Sambamba tools
• renamed CheckSex protocol to GenderCheck
• Splitted the metrics calculations
• added CramConversion (turned off in workflow)
• added CoveragePerTarget
• updated to new compute version v15.12.4
• upgraded to Java 8

Minor changes + bugfixes

• fixed GenderCheck for a WGS sample
• extended walltime for Delly and added more memory
• changed PERCENTAGE_DUPLICATES to PERCENT_DUPLICATION in dedup metrics (QC report)
• added new batch options (per chr or 1 batch)
• added #string project to every protocol
• fixed VariantCalling bug (sex is Unknown bug)

Demultiplexing pipeline 2.1.0

Added automated scripts to start the pipeline automatically when the sequencer is finished.

small bugfixes

NIPT-v3.0.1

Made a pipeline that is getting the Utrecht data out of the sFTP, then filter the data and run a tool (NIPTeR) that does the calculation and finally creating a html and pdf file

Demultiplexing pipeline 2.0.2

Fix for 5GPM samples (with no barcode)

NGS_DNA-3.1.2 pipeline (Bison)

• UPDATED the old version numbers, newest NGS_DNA version is now in the directory NGS_DNA
• added DellyAnnotator
• fixed >200-samples issue
• added pipeline version to QCReport
• bugfixes
• removed IndelRealigment step
• splitted collect metrics step into 4 steps

Demultiplexing pipeline 2.0.1

rewrote protocols written in freemarker template to bash code