Snakemake for HPC Workflows

Content

Current HPC workflows can become quite complex, beyond the scope of simple bash scripting or scheduler job dependencies. Snakemake introduces robust tools to generate elaborate workflows, including stage-in and -out options, and interaction with different job schedulers. Snakemake is particularly popular in the field of Bioinformatics, so researchers of this field will profit from attending the course. AI/ML is another discipline that can benefit from organizing job dependencies. In general, the content and experience gathered in this course should be applicable to any discipline where complex interactions between files and jobs and different stages of analysis are involved. The course will consist of an introduction to Snakemake, its concepts and capabilities, as well as 1 or 2 exercises where users will have to develop and apply their own workflows for a Bioinformatics and/or AI/ML task.

Learning goal

• How to use snakemake to generate hpc workflows
• Examples from bioinformatics and machine learning fields, but content should be applicable to any discipline

Skills

Trainer

• Dr. Martin Leandro Paleico

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