add sarscov2_nextstrain workflow #204
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…due to gisaid size increasing
…ation, make out_basename optional, copy relevant python code inline and use python:slim container, increase default RAM
…r slow becase of the implementation of --min-length in augur filter)
…k contents for faster dev cycle
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This PR adds:
And bumps the nextstrain/base docker image.
The
nextstrain_build_subsampletask subsamples a large fasta+metadata data set to a small fasta file using a nextstrain/ncov style yaml build definition. It takes a builds.yaml and build_name as input and uses them to execute the subsampling snakemake rules in the ncov repo using the nextstrain docker. This includes the ability to have arbitrarily complex subsampling schemes and heirarchies, as well as the use of the snp-distance-based priorities.py weighted sampling schemes. It is relatively sarscov2-specific at the moment.The sarscov2_nextstrain workflow is similar to the augur_from_assemblies workflow but uses the build-yaml based subsampling instead of the custom subsampling we had implemented ourselves. Since it is based on the ncov repo it has a number of sarscov2 assumptions built in.
This PR additionally adds the
augur frequenciesoutput to sarscov2_nextstrain and augur_from_assemblies.