Analysis and computational expertise
In the previous posts, we saw how to get started with snakemake, reduce command-line options, submit your jobs to a cluster, define resources and threads and handling memory and timeout errors. In this last post about snakemake profiles, I will show how to use singularity containers. If…
In the previous posts, we saw how to get started with snakemake, reduce command-line options, submit your jobs to a cluster and define resources and threads. However if one of your jobs fails because it uses more memory or time than requested, with what was covered so far, snakemake will…
The power of snakemake is to enable parallelization. Through the use of a cluster, jobs can be processed in parallel automatically. One needs to define how snakemake will handle the job submission process. If you already followed the two first posts (1,2), you can skip the first section.…
A profile is a folder that contains all the configuration parameters to successfully run your pipeline. Of note, if you have used a cluster.json file before, be aware that it has been deprecated. Preparation of files (if you skipped the first post) Run the following script to create the folder…
This blog post is the first of a series on creating snakemake profiles. Some content was directly copied from the snakemake manual. It is supposed that the reader has some basic concepts of snakemake, even if I start from the very beginning. Introduction Adapting Snakemake to a particular…