mageck-nf

DEPRECATED: Use zuberlab/crispr-mageck-nf

Statistical Analysis of multiplexed CRISPR/shRNA Screens using MAGeCK

Installation

Install Nextflow following the instructions at https://www.nextflow.io/docs/latest/getstarted.html

The most convenient way is to install mageck-nf is to use nextflow's built-in 'pull' command

nextflow pull zuberlab/mageck-nf

Computing Environment

Docker

Execute pipeline using the pre-built docker container. You must have docker installed.

nextflow run zuberlab/mageck-nf -profile docker

Singularity

Execute pipeline using the pre-built docker container with singularity. You must have singularity >= 2.4 installed.

nextflow run zuberlab/mageck-nf -profile singularity

Miniconda

Install Miniconda following the instructions at https://conda.io/docs/user-guide/install/index.html

Create a virtual enviroment using the environment file in the git repository.

conda env create --file environment.yml

Activate the environment using

source activate mageck-nf

Execute the pipeline in the virtual enviroment.

nextflow run zuberlab/mageck-nf -profile conda

Documentation

nextflow run zuberlab/mageck-nf --help

Credits

Nextflow: Paolo Di Tommaso - https://github.com/nextflow-io/nextflow

MAGeCK: Wei Li / Shirley Liu - http://mageck.sourceforge.net