Fix: update dropped strains file to list accession instead of strain names

[j23414]

Description of proposed changes

In the phylogenetic workflow, we initially listed strains slated to be dropped from the build (due to excessive divergence or misclassification) in the config/dropped_strain.txt file, identified by their strain names. Subsequently, we transitioned to using "accession" numbers to identify strains after merging the ingest pipeline (and using ncbi-datasets api) 8ab810f. However, updating the corresponding dropped strain list was missed resulting in these strains not being appropriately dropped from the build.

This commit addresses this issue by adding accession numbers to ensure proper dropping of these records.

Steps to find accessions:

• For strain whose names exactly match those in the fauna metadata.tsv file, the associated accession numbers are used.
• A visual check is performed for the remaining strains, identifying similarly named strains
  (e.g. DAK_Ar_510 is probably a shorter name for DENV2/COTE_D_IVOIRE/DAKAR510/1980)
• Strains are cross-referenced against the ingest metadata.tsv file for those collected in the same year and country, considering potential differences in underscores or hyphens separating the strain name (e.g. DENV1/VIETNAM/BIDV992/2006 equivalent to DENV-1/VN/BID-V992/2006).
• Perform a rough search of dengue academic papers to find a similarly named strain, and reference to an accession number. (e.g. A search for DENV/SPAIN/EEB17/2009 led to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149010/ which led to accession number JF260983)

Related issue(s)

• Bug: Update dropped strains file to list accession instead of strain #24

Checklist

• Checks pass

Post Merge rebase and update checklist

• Add workflow for producing the Nextclade dengue dataset #25
• Add E gene trees #18

[victorlin]

Wow, this looks like some manual work! I haven't changed these files before. Added some non-blocking suggestions from my perspective.