Summary and Schedule

This is a new lesson built with The Carpentries Workbench.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Introduction	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?
Duration: 00h 06m	2. Project Setup	How do I create a directory with the necessary files for this class?
Duration: 00h 12m	3. Environment Setup	How do I setup an shell environment to use Snakemake?
Duration: 00h 20m	4. Create a Workflow	How do you create a Snakemake Workflow? How do you run a Snakemake Workflow?
Duration: 00h 36m	5. Add an R Script	How can I create a rule using an RStudio friendly R script? How can I control what files Snakemake creates?
Duration: 00h 54m	6. Process multiple files	How can I check a Snakefile without running the whole workflow? How can I create a generic rule that can process multiple files? How can I use a python function as part of a rule? How do I tell snakemake to create a certain file before running a python function?
Duration: 01h 16m	7. Use a container	How can I make my workflow more reproducible? How do you use a docker image with Snakemake? How do I enable containers with snakemake?
Duration: 01h 24m	8. Reuse another workflow	What is needed to re-use another Snakemake workflow?
Duration: 01h 33m	9. Add Summary Analysis	How can we specify a rule that has many dynamic input files?
Duration: 01h 39m	10. Run at Scale	How can I efficently scale up my workflow in a cluster?
Duration: 01h 53m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Request OSC Access

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This workshop requires access to the OSC cluster. Please contact Matthew Thompson to request access.