Release notes Biopet version 0.6.0

General Code changes

Refactoring Gentrap, It's modules can now be used outside of gentrap also
Added more unit testing
Upgrade to Queue 3.5
MultisampleMapping is now a base for all multisample pipelines with a default alignment step

Gears: Metagenomics NGS data. Added support for 16S with Kraken and Qiime
Raise an exception at the beginning of each pipeline when not using absolute paths
Moved Varscan from Gentrap to Shiva (Varscan can still be used inside Gentrap)
Gentrap: now uses shiva for variantcalling and produce multisample vcf files
Added Bowtie 2
Added fastq validator, flexiprep now aborts when a input file is corrupted
Added optional vcf validator step in shiva
Added optional Varda step in Toucan
Added trimming of reverse complement adapters (flexiprep does this automatic)
Added Tinycap for smallRNA analysis
Gentrap: Refactoring changed the "expression_measures" options
Fixed biopet logging
Added sample tagging
Seqstat now reports histogram of read lengths
Fixed bug in seqstat when having multiple sizes exists in the fastq file
Added variant plots for targets to report of Shiva
Adapter feed to cutadapt now use only that parts that are reported by fastqc and not the full sequence
Added a reference selector when fasta file can't be found. User now get a list of available species and genomes in the config
Fixed bcftools with IUPAC symbols

Development environment within the LUMC is now tested with Jenkins
- Added integration tests for Gentrap
- Added integration tests for Gears
- Added general MultisampleMapping testing