Welcome to MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

Automizing HTS analysis from data download, preprocessing and mapping to postprocessing/analysis and track generation centered on a single config file. MONSDA can create Snakemake and Nextflow workflows centered on a user friendly, sharable Json config file and reproducible subworkflows. These workflows can either be saved to disk for manual inspection and execution or automatically executed.

For details on Snakemake and Nextflow and their features please refer to the corresponding Snakemake or Nextflow documentation.

In general it is necessary to write a configuration file containing workflows to execute, information on paths, files to process and settings beyond default for mapping tools and others. The template on which MONSDA is based on can be found in the config directory.

For MONSDA to be as FAIR as possible, one needs to use conda or the faster drop-in replacement mamba. For details on either please refer to the corresponding conda or mamba manual.

This workflow organizer makes heavy use of conda and especially the bioconda channel.