phylogenetic: Support nextstrain run (alternative)
#330
Conversation
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
2 tasks
joverlee521
force-pushed
the
nextstrain-run-workflows
branch
2 times, most recently
from
94b2159 to
d7722ce
Compare
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.
joverlee521
force-pushed
the
nextstrain-run-workflows
branch
from
57e52de to
9cac7a4
Compare
Follow the latest format expected in nextstrain/cli@f04761d
35 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
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.
Checklist