install.md

Install Nextflow

To run Nextflow it needs to be executable on the command-line. On an environment module system such as the one at The Francis Crick Institute this can be achieved by running the following command:

module load nextflow/0.30.2

You need Nextflow version >= 0.30.2 to run this pipeline.

See nextflow.io for further information on how to install Nextflow.

Obtaining the pipeline

There are various ways in which you can obtain the pipeline itself, however we recommend that you obtain a local copy of the pipeline by running the following git command in a directory where you want to perform the analysis:

git clone https://github.com/crickbabs/BABS-MNASeqPE

The Nextflow pipeline and associated config and executable files will appear in the BABS-MNASeqPE/ directory.

cd BABS-MNASeqPE

You can now configure the pipeline to run on a Linux system of your choice. See Pipeline configuration and Reference genome sections.