Nextflow supports fetching nearly everything it needs to run a pipeline over the web automatically: pipeline code, software requirements, reference genomes and even remote data sources.

If you need to run your analysis on a system that has no internet connection, don't panic! There are just a few extra steps required to get everything you need available locally.

Nextflow

First of all, you need to have Nextflow installed on your system. Go to the Nextflow releases page on GitHub: https://github.com/nextflow-io/nextflow/releases. Each release has a dropdown with associated Assets. One of these should have the suffix -all, e.g. nextflow-19.10.0-all. Download this file and transfer to your offline system. Run it to install Nextflow (it is a very large bash file).

Once installed, you can stop nextflow from looking for updates online by adding the following environment variable in your ~/.bashrc file:

export NXF_OFFLINE='TRUE'

Pipeline code

To run a pipeline offline you need the pipeline code, the software requirements and the shared nf-core/configs configuration profiles. To help with this process, we have created a helper tool as part of the nf-core package to automate this for you.

On a computer with an internet connection, run nf-core download <pipeline> to download the pipeline and config profiles. Add the argument --singularity to also fetch the singularity container (requires Singularity to be installed on your system).

The pipeline and requirements will be downloaded, configured with their relative paths and packaged in to a .tar.gz file by default. This can then be transferred to your offline system and unpacked.

To run the pipeline, simply do nextflow run <directory>

For more information about the nf-core helper tools, see the documentation.

Reference genomes

Some pipelines require reference genomes and have built-in integration of AWS-iGenomes. If you wish to use these references you must download them and transfer to your offline cluster. Once transferred, follow the reference genomes documentation to configure the base path for the references.