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View Code? Open in Web Editor NEWNextflow implementation of Nextstrain's Augur pipeline
Nextflow implementation of Nextstrain's Augur pipeline
This is really cool! We're super excited to see nextstrain being used by different groups.
Small point of terminology: there is no such thing as the "augur pipeline" -- augur is a set of tools which can be put together to create any number of pipelines. (If we have ever used this terminology please let me know & I'll update it ASAP.) A pipeline should describe the analysis it is intended for, which is typically specific to the pathogen, available metadata etc. For instance https://github.com/nextstrain/zika and https://github.com/nextstrain/tb contain different pipelines, each of which uses augur commands.
cc @garfinjm who maintains a fork of this at https://github.com/garfinjm/augur-nf, but creation of issues is disabled on that repo.
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