Category: Snakemake


Building Snakemake Command Line Wrappers for Kubernetes Workflows

Posted in Snakemake

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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.

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