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{:bash}

:map

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

inputs{:bash}

:file

Any input file required by Snakemake

*

meta2{:bash}

:map

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

snakefile{:bash}

:file

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

Output

name:type
description
pattern

outputs{:bash}

meta{:bash}

:map

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

[!.snakemake|versions.yml]**{:bash}

: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{:bash}

meta{:bash}

:map

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

.snakemake{:bash}

:directory

Hidden directory containing Snakemake execution logs and metadata

.snakemake

versions_snakemake{:bash}

${task.process}{:bash}

:string

The name of the process

snakemake{:bash}

:string

The name of the tool

snakemake --version{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

snakemake{:bash}

:string

The name of the tool

snakemake --version{:bash}

:eval

The expression to obtain the version of the tool

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
maintainer
Github user adamrtalbot
get in touch
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