Release notes Biopet version 0.4.0

  • A reporting framework has been added for most pipelines
  • This framework produces a static HTML report which can be viewed in your browser
  • The framework contains lots of quality control and downstream analyses plots (genome coverage, transcript coverage etc etc.)
  • An issue where a NullPointerException was being thrown when output_dir was not set in the config was fixed. This now gives a nice error message which points to the missing key in the config
  • Pipelines now automatically write a log file if none is specified on command line
  • Tools writing to VCF will no longer fail when the output is not a gzipped VCF
  • Pipelines now support passing config options directly into the commandline prompt
  • Pipelines now support a more readable config file format YAML
  • Memlimit and vmem memory issues are solved by automatically increasing the amount of available memory when a job fails. --retry 5 should do the trick
  • BamMetrics pipeline is updated to work with newest version of Picard
  • A bug in VcfStats in comparing samples alleles is fixed. Now each allele can only be used once in the comparison.
  • VcfStats is now capable of summarizing stats per bin (bin size is changeable)
  • There is now a module which checks for the present of correct reference files if not it automatically builds the appropriate ref files

Some pipelines were updated as well:

  • Gentrap
  • Shiva