ADM5 Workflow Management Systems - Snakemake

Snakemake offers to setup a system-wide configuration file, selecting the default excecutor (Snakemake lingo for the execution of job, e.g. for cloud systems or HPC batch sytems) or defining remote file paths (e.g. to stage-in and out data “automagically”).

• USE6.3 Workflow Parameterization for HPC Clusters

• Identify Snakemake's capabilities for configuring its behaviour across a cluster environment.
• Configure and set-up a cluster-wide YAML-based configuration file for Snakemake that will not interfere with other systems (e.g. CWL or Nextflow) and helps avoiding performance issues such as I/O contention.