Oxford Nanopore SARS-CoV-2 data processing using the ARTIC pipeline

This repository provides a WDL wrapper for running the Connor lab's implementation of the ARTIC pipeline to process Oxford Nanopore single-ended SARS-CoV-2 sequencing data.

Workflow inputs

An input template file with some defaults pre-defined can be found here.

Input	Description
accession	Sample ID
fastqs	Array of single-ended FASTQ files
primer_version	The ARTIC primer version used to prepare the Nanopore library. Must be one of the schemes included in the official ARTIC network repository. Can be specified either as "ARTIC Vx" or as "Vx"
min_length	Minimum allowed read length for artic guppyplex [400]
max_length	Maximum allowed read length for artic guppyplex [700]
min_reads	Minimum number of reads output by artic guppyplex to pass QC. The workflow will exit with an error if this read count is not met.
container_registry	Registry that hosts workflow containers. All containers are hosted in DNAstack's Dockerhub [dnastack]

Workflow outputs

Output	Description
consensus_fa	Genome assembly
vcf, vcf_index	Variant calls and index
bam	Reads aligned to the SARS-CoV-2 reference genome
summary	Pipeline metrics and plots

Containers

Docker image definitions can be found in our bioinformatics-public-docker-images repo.

The pipeline will always be pegged to a specific ncov2019-artic-nf commit hash to avoid breaking due to updates to the underlying pipeline. The pipeline is periodically updated to the most recent version of the ncov2019-artic-nf pipeline.

All containers are publicly hosted in DNAstack's container registry.