Closed j23414 closed 3 months ago
This PR so-far creates a Nextclade dataset
but is stuck on the following errors when testing the assembled dataset:
nextstrain build nextclade test_output/all
nextstrain build nextclade test_output/denv1
nextstrain build nextclade test_output/denv2
nextstrain build nextclade test_output/denv3
nextstrain build nextclade test_output/denv4
Because I fear inadvertently wandering off the path of acceptable solutions, it might be most helpful and efficient for someone(s) with more experience to submit commits to this branch. From the changes, we can have a productive discussion. Please feel free to message me if anyone wants a zipped folder of the results.zip intermediate files.
After some discussion with a few people, I may move the 'fine-tuning' of the "dengue/all" dataset commits to a new draft PR since we are still testing solutions.
This approach allows us to merge a functional workflow for assembling a Nextclade dataset, providing a base from which we can test different solutions. @joverlee521, this scoped PR is ready for review
if we can just drop nextclade/datasets/
Yes, I wondered that as well. But then decided to keep it as a foundation for a "fine-tuning" PR or for others who might want to create separate branches to explore different solutions from the existing dataset.
My plan is to delete this when https://github.com/nextstrain/nextclade_data/pull/203 is finalized and merged.
Description of proposed changes
Introduce a workflow dedicated to generating the Nextclade dataset for dengue serotypes and
subtypesgenotypes. This workflow will be housed in a designatednextclade
folder, aligning with the pathogen-repo-guide/nextclade. This workflow is for streamlined dataset creation, testing, and debugging.The changes can be summarized as follows:
nextclade
directory to adhere to the pathogen-repo-guide/nextclade. Start with a copy of the Nextclade README from thepathogen-repo-guide/nextclade
repository.tree.json
files.pathogen.json
). Rules copied from mpox.Related issue(s)
Checklist