Reference

Glossary

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• Snakemake

A free software application, written in Python, which knows how to read and execute Snakefiles. Once installed, it is invoked from the shell via the snakemake command.

• Snakefile

A text file containing one or more rule definitions which may be invoked to make a workflow. The file may also hold variables, functions and other settings.

• Workflow

A series of jobs that are to be executed in a suitable order to generate a final target output. Snakemake plans the workflow based upon the Snakefile, the configuration, and the target, so a single Snakefile may define multiple possible workflows.

• DAG

Directed Acyclic Graph. An internal representation of the jobs in a workflow and how they depend on one another. It may be visualised as a diagram of boxes connected by arrows.

• Rule

A recipe telling Snakemake how to generate some particular type of file, normally by running a shell command on one or more input files.

• Job

A concrete task in a workflow, also called a Step in the Snakemake logs. A job is defined by a rule plus specific wildcard values, so each rule may yield many jobs.

• Conda

A package installation system derived from the Anaconda distribution, which allows for management of self-contained software environments and backed by a large repository of community maintained packages.

• Cluster

A computer system comprised of multiple processing nodes, connected to a shared storage system and supporting the running of batch jobs via a cluster manager. When run with appropriate settings on a cluster, Snakemake can turn its own jobs into cluster batch jobs and submit and monitor them automatically.

• YAML

A way to express structured data within a text file. Snakemake uses this format for configuration files, and Conda uses it for exporting and importing environment definitions.

• Escaping

With regard to the text within a Snakefile, a way to indicate that certain characters should not be treated as having a special meaning. A typical example would be "\t" versus "\\t", where the first string represents a tab character, but the second represents a backslash character followed by a letter ‘t’, and the extra backslash is referred to as an escape character.