A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Adding necessary changes for the pipeline to work with sc2reporter. Mainly qc files, freebayes and VEP. The gff previously in the repo had some formatting I have never seen before so I changed it to what we are using. If this breaks nanopore workflows then we should separate the two gffs or see if there is a way to use one version.
Adding necessary changes for the pipeline to work with sc2reporter. Mainly qc files, freebayes and VEP. The gff previously in the repo had some formatting I have never seen before so I changed it to what we are using. If this breaks nanopore workflows then we should separate the two gffs or see if there is a way to use one version.