Register workflows in nextstrain-pathogen.yaml#69
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joverlee521 merged 2 commits intomainfrom Sep 26, 2025
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victorlin
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Tested with Nextstrain CLI 10.3.0 and #74, works well.
Before:
$ nextstrain run . phylogenetic ./tmp
The 'phylogenetic' workflow is not registered by pathogen '.'!
Trying to run it anyways (but it likely won't work)…
Running the 'phylogenetic' workflow for pathogen .
Resolved 'include_strains_genome.txt' to '/nextstrain/pathogen/phylogenetic/defaults/include_strains_genome.txt'.
Resolved 'include_strains_N450.txt' to '/nextstrain/pathogen/phylogenetic/defaults/include_strains_N450.txt'.
Resolved 'dropped_strains.txt' to '/nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt'.
Resolved 'dropped_strains.txt' to '/nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt'.
Saved current run config to 'results/run_config.yaml'.
After:
$ nextstrain run . phylogenetic ./tmp
Running the 'phylogenetic' workflow for pathogen .
Resolved 'include_strains_genome.txt' to '/nextstrain/pathogen/phylogenetic/defaults/include_strains_genome.txt'.
Resolved 'include_strains_N450.txt' to '/nextstrain/pathogen/phylogenetic/defaults/include_strains_N450.txt'.
Resolved 'dropped_strains.txt' to '/nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt'.
Resolved 'dropped_strains.txt' to '/nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt'.
Saved current run config to 'results/run_config.yaml'.
victorlin
reviewed
Sep 26, 2025
Depends on merge and release of nextstrain/cli#472
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Description of proposed changes
Depends on merge and release of nextstrain/cli#472Requires Nextstrain CLI 10.3.0
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