CWL viral pipeline

CWL implementation of the MGnify viral pipeline.

Setup

It is possible to run the pipeline using docker/singularity or a conda env.

Install conda and create an env using the conda_env.yml file:

Rename the path in requirements/conda_env.yml to the desired env path

conda env create -f requirements/conda_env.yml

The init.sh file is meant to set some env variables needed for the execution, this script is called from virify.sh.

After installing docker or singularity you will need some python package in you system:

pip install -r requirements/pip_requirements.txt

In order to run the pipeline the following databases are required:

Everything is packed and ready to be used from EBI FTP:

./download-databases.sh -h

Download VIRify DBs for the CWL version
* requires rsyncimgvr_blast_swf.cwl

-f Output folder [mandatory]

The pipeline users toil as the CWL execution engine.

In order to run it use the helper script (provided you adjusted the paths on it).

$ ./virify.sh -h

CWL tests are executed with cwltest.

Run:

cd tests
./cwltest.sh