Configuration - FranckLejzerowicz/metagenomix GitHub Wiki

Creating a pipeline relies on multiple configurations files:

Mandatory

  • metadata: sample metadata file with the sample name as first column
  • pipeline: defined the sequence of softwares to run and in which order
  • databases: paths to the database names that may be used by the pipeline softwares

Optional

  • parameters: user-defined parameters for the software and their resource needs (for HPC jobs)
  • modules: names of the modules to load (module load <name>) for the pipeline softwares
  • co-assembly: groups of metadata variable factors defining samples to assemble together
  • strains: lists of species names for which to run strain-level analyses
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