Support nextstrain run (with YAML-configured augur filter)#106
Closed
victorlin wants to merge 5 commits into
Closed
Support nextstrain run (with YAML-configured augur filter)#106victorlin wants to merge 5 commits into
victorlin wants to merge 5 commits into
Conversation
This improves readability of the main Snakefile, especially with more config-related operations in mind. phylogenetic/rules/config.smk # deleted: phylogenetic/rules/write_config.smk #
This is an alternative to using augur subsample.
…/vendored subrepo: subdir: "shared/vendored" merged: "2d063cf" upstream: origin: "https://github.com/nextstrain/shared" branch: "main" commit: "2d063cf" git-subrepo: version: "0.4.9" origin: "https://github.com/ingydotnet/git-subrepo" commit: "4f60dd7"
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 not strictly necessary, but
consolidates 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
This was referenced Sep 18, 2025
Member
Author
|
#96 is merged so this is no longer relevant. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Alternative to #96 + #105.
The only real difference is 89ae094 instead of #96. All the other changes are effectively the same.