This is a list of example workflows exemplifying the use of Cuneiform for different use cases. All workflows come in the form of a Chef cookbook, which automatically sets up the workflow, fetches all input data, and sets up all necessary tools.

Machine Learning and Information Retrieval

Bioinformatics and Next-Generation Sequencing

  • Phylogeny https://github.com/joergen7/phylogeny
  • GC Count https://github.com/joergen7/gccount
  • ChIP-Seq https://github.com/joergen7/chip-seq
  • Variant Calling (GATK) https://github.com/joergen7/variant-call-gatk
  • RNA-Seq https://github.com/joergen7/rna-seq
  • Variant Calling (VarScan) https://github.com/joergen7/variant-call
  • Methylation Analysis https://github.com/joergen7/methylation