Description

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. This module runs a simple Snakemake pipeline based on input snakefile. Expect many limitations.”

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

inputs (file)

Any input file required by Snakemake

*

meta2 (map)

Meta information for Snakefile
e.g. [ id: ‘snakefile’ ]

snakefile (file)

Snakefile to use with Snakemake. This is required for proper execution of Snakemake.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

outputs (file)

Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated.

snakemake_dir (directory)

Snakemake log directory (.snakemake). Can be used to capture logs of Snakemake execution.

versions (file)

File containing software versions

versions.yml
author
Github user adamrtalbot
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Tools

snakemake
MIT

A popular workflow management system aiming at full in-silico reproducibility.

snakemake.readthedocs.io/en/stable https://github.com/snakemake/snakemake 10.1093/bioinformatics/bty350