Add workflow for producing the Nextclade dengue dataset

[j23414]

Context

Add a workflow for producing the Nextclade dataset for dengue serotypes and subtypes in a nextclade folder, following the pathogen-repo-guide. This will ease dataset creation, testing, and debugging.

Description

TBD

Examples

Possible solution

TBD

[j23414]

For reference strains separating out DENV1-DENV4 (KM204119, KM204118, KU050695, and KR011349)) based on the following publication:

Añez, G., Heisey, D.A., Volkova, E. and Rios, M., 2016. Complete genome sequences of dengue virus type 1 to 4 strains used for the development of CBER/FDA RNA reference reagents and WHO international standard candidates for nucleic acid testing. Genome announcements, 4(1), pp.10-1128.

[j23414]

Documenting plan of work in the issue instead of scattered across PRs:

• [x] Create a PR to prepare phylogenic workflow to be compatible with the nextclade workflow
  • [x] augur translate rooting to be compatible with https://github.com/nextstrain/nextclade/pull/1455
  • [x] add a configurable includes.txt to force-include key strains (e.g. vaccine-related, lineage-defining)
• [x] Rebase existing Nextclade dataset workflow PR
  • [x] move shared resources into a dedicated "shared" directory b.c. 10 trees :lolcry: -> have nextclade workflow link to config and bin dir in phylogenetic since most should be the same.
  • [x] Ask for expertise contributions from Nextclade Subject-Matter-Experts (SME)
• [ ] Use Sidney's strain_genotypes.tsv as the source of truth for Nextclade datasets in a separate PR
  • [ ] Copy to config folder
  • [ ] Map to Genbank accession to populate the includes.txt for the Nextclade workflow