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.
In total there are four profiles that control how to run modules. We recommend:
Which were described in the profiles section.
We also provide:
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
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