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  • container - Containers are like very lightweight virtual machines that can provide an isolated, consistent, reproducible environment in which to run software.

  • directive - this refers to subheadings of rules, such as input: or output: or shell:

  • docker - Docker is a program that allows running containers. Docker is very popular in enterprise software engineering, but presents challenges for scientific computing because it requires an admin account and presents security risks, making it hard to run in an HPC environment.

  • rule - Snakemake rules define a given task, the input files it depends on, the output files it produces, the shell commands it should run, etc.

  • singularity - Singularity is a program that allows running containers, like Docker, but without requiring an admin account and without many of the security concerns that Docker creates.

  • Snakefile - Snakemake is a Python program that is used to run a set of commands in a file; Snakefile is the default name of the file in which Snakemake expects to find those definitions.