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Old 12-05-2013, 02:24 AM   #1
johanneskoester
Junior Member
 
Location: Germany

Join Date: Sep 2011
Posts: 2
Default A new release of the Snakemake workflow system

Hi guys,
I would like to announce version 2.4.8 of Snakemake.
Snakemake is a pythonic text-based workflow system with a clean and easy to read language for defining your workflows. Snakemake is inspired by GNU Make. Workflows are defined by rules, that generate output files from input files. Rule dependencies and parallelization are automatically determined by Snakemake.
In contrast to GNU Make, Snakemake allows to have multiple output files in a rule. Further, rules can use shell commands, Python, or R code. Snakemake provides many additional useful features like resource-aware scheduling, parameter- and version-tracking and detection of incomplete files.
Finally, Snakemake has a generic cluster support, that works with any cluster or batch system that provides a qsub-like command and a shared filesystem.

To give you an impression, this is how Snakemake rules look like:
Code:
rule targets:
    input:  'plots/dataset1.pdf', 
            'plots/dataset2.pdf'

rule plot:
    input:  'raw/{dataset}.csv'
    output: 'plots/{dataset}.pdf'
    shell:  'somecommand {input} {output}'
If you like Snakemake, please feel free to visit http://bitbucket.org/johanneskoester/snakemake.
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