phylogenetic: Support nextstrain run (alternative)#330
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joverlee521 wants to merge 4 commits intomasterfrom
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phylogenetic: Support nextstrain run (alternative)#330joverlee521 wants to merge 4 commits intomasterfrom
nextstrain run (alternative)#330joverlee521 wants to merge 4 commits intomasterfrom
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Use the `nextstrain-pathogen.yaml` to declare the ingest workflow as a `nextstrain run` compatible workflow. Requires changes from <nextstrain/cli#461> to properly list the workflow in the Nextstrain CLI outputs.
Mostly workflow path updates to support `nextstrain run`. This should allow the default phylogenetic build to run with `nextstrain run mpox phylogenetic <analysis-dir>`. The following commit will add support for the other builds.
Use the `nextstrain-pathogen.yaml` to list the available phylogenetic workflows for `nextstrain run`. Requires changes from <nextstrain/cli#462> to properly use the correct Snakefile and configfile for each workflow.
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Follow the latest format expected in nextstrain/cli@f04761d
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Description of proposed changes
An alternative to #327, where instead of maintaining a separate Snakefile per named phylo workflow, we just define the phylo workflows in the nextstrain-pathogen.yaml. Depends on CLI changes in nextstrain/cli#462.
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