search

connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
88 stars 89 forks source link

Sc2reporter comp #127

Closed LordRust closed 2 years ago

LordRust commented 2 years ago

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.

LordRust commented 2 years ago

Made an error and sent the pull request here. Please disregard