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Objectives

Tools to make processing and analysis reproducible

Outline

1hr workshop

40min talk, 20min Q&A

two docs

• env creation
• snakemake steps

Conda, 20 mins

• What is a virtual environment

• how conda env works

  • conda channel and pre-built packages
  • filetree structure

• conda commands

  • creating env
  • searching for and installing a package from a channel

Snakemake, 20 mins

• What is a pipeline

• What is a pipeline orchestrator and why do you need it

  • reproducibility

• Structure of a snakefile

• Demo

• Cache inheritance

• Early detection

• Experiments