A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
In a large scale production environment, it is desirable to minimise the number of steps in the workflow, to avoid internet access, and to avoid re-creation of the same output files for every run of the workflow, which may get run thousands of times.
To this end, this PR enables 2 modes.
In the first, you can supply --schemeRepoURL /path/to/own/clone/of/github.com/artic-network/artic-ncov2019. This stops the git clone step, and you can run the workflow many times on a known fixed revision of the repo.
In the second, you can supply both --ivarBed /path/to/ivar-compatible.bed and --alignerRefPrefix /path/to/bwa-indexed/ref.fa. This also stops the reference fasta from being reindexed all the time.
In a large scale production environment, it is desirable to minimise the number of steps in the workflow, to avoid internet access, and to avoid re-creation of the same output files for every run of the workflow, which may get run thousands of times.
To this end, this PR enables 2 modes.
In the first, you can supply
--schemeRepoURL /path/to/own/clone/of/github.com/artic-network/artic-ncov2019. This stops thegit clonestep, and you can run the workflow many times on a known fixed revision of the repo.In the second, you can supply both
--ivarBed /path/to/ivar-compatible.bedand--alignerRefPrefix /path/to/bwa-indexed/ref.fa. This also stops the reference fasta from being reindexed all the time.