Tag: workflows

Building Snakemake Command Line Wrappers for Kubernetes Workflows

Posted Monday 01/28/2019 in Snakemake

NOTE: These ideas are implemented in the repository charlesreid1/2019-snakemake-byok8s.

Recap: Workflows as Executables

In our previous blog post, Building Snakemake Command Line Wrappers we covered some approaches to making Snakemake workflows into …

Tags: python bioinformatics workflows pipelines snakemake travis kubernetes minikube

Building Snakemake Command Line Wrappers for Workflows

Posted Monday 01/21/2019 in Snakemake

NOTE: These ideas are implemented in the repository charlesreid1/2019-snakemake-cli.

Table of Contents

Basic Idea: Wrapping Snakemake API Calls
- 2018-snakemake-cli
- 2019-snakemake-cli
Turning Executables into Packages
End Result: Using bananas
Adding Travis CI Tests
Final Repository
Next Steps

Basic Idea: Wrapping Snakemake API Calls

2018-snakemake-cli

This blog post covers the implementation of an idea that was originally explored in a blog post from Titus Brown, Pydoit, snakemake, and workflows-as-applications.

That blog post implemented a basic command line wrapper around the Snakemake API to demonstrate how a Snakemake workflow could be …

Tags: python bioinformatics workflows pipelines snakemake travis