Support nextstrain run (with augur subsample)#105
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Update all workflows to support nextstrain run. Instead of applying
resolve_config_path() in individual rules, resolve them all at once at
the start of the workflow. This is the only way I can think of to have
nextstrain run compatibility with augur subsample. It also has a nice
side effect of consolidating code changes to a single function instead
of all rules that take file paths from config.
🚧: update the Nextclade workflow?
Testing commands:
mkdir -p ~/.nextstrain/pathogens/wnv
ln -sv ~/repos/nextstrain/wnv ~/.nextstrain/pathogens/wnv/local=NRXWGYLM
nextstrain run wnv@local phylogenetic ./tmp
References:
- nextstrain/mumps@6343dd8...0866a88
- nextstrain/zika@5041a36...e4f084d
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tsibley
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Sep 24, 2025
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nextstrain/measles#74 has an updated version of the filepath resolving function ( |
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Supporting |
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Description of proposed changes
The nextstrain run command allows users to run the workflows in this repository without cloning or forking it.
Related issue(s)
Based on similar work in other repos (zika, mumps) with some new ideas.
See #106 for a version of this PR without using
augur subsample.Checklist
nextcladedirectory #95