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nextstrain / seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds
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Nextclade #124

Closed rneher closed 11 months ago

rneher commented 12 months ago

Adds a workflow to produce nextclade data sets

rneher commented 11 months ago

we'll release an alpha version in 10 days or so. until then, you can either build it or get if from the CI artefacts. Tom linked to them in slack.

rneher commented 11 months ago

most of these changes are unrelated to the main workflow. I vote for merging this soon to avoid the complications with divergent branches.

huddlej commented 11 months ago

@rneher The workflow runs for me now as expected, with the few changes I made above. I tested one of the datasets generated by the workflow (datasets/h1n1pdm/ha/CY121680) with one of the Nextclade UI prototypes and got the following error about parsing the pathogen JSON:

image

We could merge this PR and keep working on it from master or we could pull the main workflow changes out of this PR into master and keep working here. Eventually people might start depending on the nextclade workflow to work on master, but I doubt anyone will right now since it's new.

rneher commented 11 months ago

thanks John. I think this error you got should not happen with the most recent version. I merged this now. It is a separate workflow and it we can keep improving it on master .