Tag: travis


Building Snakemake Command Line Wrappers for Kubernetes Workflows

Posted in Snakemake

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



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Recap: Workflows as Executables

In our previous blog post, Building Snakemake Command Line Wrappers, we covered some approaches to making Snakemake workflows into executables that can be run as command line utilities.

In this post, we extend those ideas to Snakemake workflows …



Tags:    python    bioinformatics    workflows    pipelines    snakemake    travis    kubernetes    minikube   


Building Snakemake Command Line Wrappers for Workflows

Posted in Snakemake

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



Table of Contents:



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 turned into an executable.

Relevant code is in ctb/2018-snakemake-cli, but the basic …



Tags:    python    bioinformatics    workflows    pipelines    snakemake    travis