snk 0.6.9

No project description provided

SNK (Snek)

---

Documentation: https://snk.wytamma.com

Source Code: https://github.com/Wytamma/snk

---

Snk (pronounced snek) is a SNaKemake pipeline management system. Snk allows you to install Snakemake pipelines as Command Line Interfaces (CLIs). Using a pipeline as a CLI increases its interoperability and allows complex pipelines to be used as modular components in a larger system. Snk, using python magic, will dynamic genrate the pipeline CLI using the pipeline configuration file.

Installation

pip install snk

Basic Use

Install a pipeline as a CLI

Install the dna-seq-gatk-variant-calling pipeline (v2.1.1) as variant-calling.

snk install snakemake-workflows/dna-seq-gatk-variant-calling --name variant-calling -t v2.1.1

Successfully installed variant-calling (v2.1.1)!

Inspect the CLI

variant-calling --help

View run options

variant-calling run -h

Create a DAG

Here we use the .test resources included in the pipeline to create the DAG.

variant-calling run -r .test/config -r .test/data --dag dag.pdf

Configure

Snk will dynamically generate config options for the CLI. For example if your config.yaml file has the option fasta: null you can set this option with --fasta.

variant-calling run --fasta example.fa

You can also configure the pipeline using a config file.

variant-calling config --pretty # print the config 
variant-calling config > config.yml # save the config 
variant-calling run --config config.yml # run with config 

how it works

When installing a pipeline snk will

• create directory $PYTHON_BIN_DIR/../snk/pipelines/PIPELINE
• install the pipeline into this directory
• expose CLI at $PYTHON_BIN_DIR that point to pipeline directory in snk/pipelines/PIPELINE/bin
• As long as $PYTHON_BIN_DIR is on your PATH, you can now invoke the pipeline globally

License

snk is distributed under the terms of the MIT license.