This repository is a Dockerized pipeline for creating consensus viral genomes from Oxford Nanopore data. This pipeline leverages the ARTIC Network bioinformatics pipeline and couples many annotation and reporting tools, resulting in an automatically generated PDF report. The pipeline is built to be deployed in the Basestack platform (https://github.com/jhuapl-bio/Basestack) so that anyone, regardless of bioinformatics expertise, can run it and make use of its automated consensus genomes and reports.
an extension of this issue - if the manifest includes a barcode that is not present in the sample, the pipeline stalls - this should fail in a way that still generates a report indicating the sample without any data
tmehoke
commented
3 years ago
nb12 vs nb24 failure if you pick the wrong one add error message if all files are empty