Add ingest

[kimandrews]

Description of proposed changes

Add ingest folder from pathogen-repo-template and make measles-specific modifications, following these steps:

• Add ingest folder from pathogen-repo-template
• Add measles-specific config parameters
• Remove files that are not currently being used for this workflow, including files related to Entrez data-fetching, Nextclade, and automation
• Remove strain name-fixing in anticipation of using accession numbers as identifiers for phylogenetic analysis
• Add NCBI Datasets "virus-name" field to metadata because it includes measles genotype identifiers

[joverlee521]

the use of the strain column as the metadata id column leads to duplicated records when running augur filter and causes the phylogenetic workflow to crash. I expect we'll need ingest to use the accession as the strain column, but that's probably something you've discussed with @j23414 and @joverlee521 already?

Overall, we are going down the route of using accession as the --metadata-id-column for Augur commands instead of the default strain field. So this will require changes in the phylo workflow that should be included in future PRs.