GenPipes is a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High-Performance Computing clusters and the cloud.  GenPipes comes with 12 validated and scalable pipelines for various genomics applications.


GenPipes features:

  • Multiple schedulers:
    GenPipes is optimized for HPC processing. It currently accommodates 4 schedulers.
  • Job dependencies:
    GenPipes establishes dependencies among its different steps. This enables launching all
  • Smart relaunch:
    GenPipes sets and detects flags at each successful step in the pipeline. This allows the detection of successfully completed steps and easy relaunch of failed steps.
  • Parameter encapsulation:
    Genpipes uses a superposed configuration system to parse all required parameters from configuration files. This simplifies the use of the framework and makes it more flexible to user adjustments. Tested configuration files that are tailored to different clusters and different species are included with GenPipes.
  • Diverse inputs:
    GenPipes has been developed to launch using different starting inputs, making it more flexible.
  • Flexible workflows:
    GenPipes implements a workflow in steps. Users can choose to run specific steps of interest, limiting waste of time and resources.


GenPipes available workflows:

  • DNA-Seq
  • DNAseq_high_coverage
  • RNA-Seq
  • De-Novo RNASeq
  • ChIP-Seq
  • Tumour Analysis
  • Hi-C
  • Metagenomic
  • PacBio assembly