Advanced installation

Clone development version

Download the most recent development version (pulling all the commits in our repository):

$ git clone https://github.com/nebfield/snpQT.git

main.nf is the entrypoint of the pipeline (e.g. nextflow run main.nf).

The development version may break randomly.

Additional profiles

In total there are four profiles that control how to run modules. We recommend:

• -profile conda
• -profile singularity

Which were described in the profiles section.

We also provide:

• -profile docker
• -profile modules

Docker requires root (superuser) access to build and run containers. We also assume that you have run the post-install steps for Linux.

Modules requires Anaconda and Environment modules to be installed, and is mostly useful for cluster environments if you can't run Singularity.

Build your own reference data (optional)

If you're feeling masochistic you can build your own reference data. This will take a decent chunk of computing power and time:

nextflow run main.nf -profile standard,conda --download_db core

This will download the core reference files, prepare them and put them in a db/ folder in the snpQT directory. On our computers it takes around an hour to run but this may take longer depending on your network. The core dataset requires about ~43GB of initial storage of intermediate files in the work/ that can be removed using nextflow run main.nf --download_db core && rm -r work and only 19.7GB of reference files that are stored in database directory db/. If you wish to build an imputation database you can alternatively use --download_db impute.