Introduction

Overview

Questions

• Why not use a general purpose language like bash or python for writing workflows?
• What problems do workflow languages solve?
• What are the strengths and weaknesses of Snakemake?
• What will be covered in this workshop?

Objectives

• Understand why one would use a workflow language like Snakemake
• Understand the goals of the workshop

Workflow Challenges

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Using a general purpose language like bash or python can be challenging:

• Not re-running the whole pipeline every time
• Adapting the pipeline to run in different environments
• Providing dependencies for tools
• Tracking progress of the workflow

Workflow language features

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• Portable
• Reproducible
• Scalable
• Reusable

List of workflow languages: https://workflows.community/systems

Strengths of Snakemake

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• Readability
• Only creates missing or out of date files
• Flexible control over which files are created
• Is python with some additional rule syntax
• Dynamic branching
  • Workflow isn’t fixed at start up.
  • Outputs of commands can be used determined what happens next.

Weaknesses of Snakemake

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• Requires learning rule based logic instead of procedural logic
• Requires some python code/knowledge for typical workflows

Class Plan

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• Create Snakemake Workflow that
  • Runs R scripts for filtering and final analysis
  • Runs Machine Learning Components
  • Efficiently processes many files at the same time
  • Reuses an existing Snakemake workflow