Exercises: General guidelines - RomainFeron/workshop-snakemake-sibdays2020 GitHub Wiki

Over the course of the workshop, we will implement and improve a workflow to align reads to a reference, call variants, and compute some statistics on these variants. The goal of the workshop is that after the last series of exercises, you will have implemented a complete workflow using many advanced Snakemake features. You will be able to use this workflow as a reference to implement your own workflows in the future.

All the software required by this workflow is already installed as part of the snakemake-workflow Conda environment.

Each section of the workshop - apart from the last one - will end with a series of exercises. You should implement these exercises in the workflow directory of this repository. You will be free to chose the names and location of output files for the different steps of your workflow. We recommend that you at least group all outputs from the workflow in a results directory within the workflow directory. You should not hesitate to modify and overwrite your code from previous questions when specified in an exercise, as we provide clean solutions for each series of exercises in the solutions directory.

We will try to cover everything needed for the exercises in the slides, but we wrote a more detailed documentation for each section in this wiki. You should use this documentation as reference when implementing the exercises.

Each series of exercises is divided in multiple questions. We first provide a general explanation on the context behind each question; we then explicity describe the task and provide details when they are required. We provided hints that should help you with the most challenging parts of some questions. You should first try to solve the problems without using these hints! If something is not clear at any point, please call us and we will do our best to answer your questions.