Switch to augur curate titlecase and format-dates subcommands

[j23414]

Description of proposed changes

As part of an ongoing migration of transform scripts to augur curate subcommands, this PR moves to replace the titlecase and format-dates scripts with their corresponding augur curate subcommands:

• augur curate titlecase
• augur curate format-dates

During the process of manual testing, an issue related to multiple headers in the fetched data was identified and resolved. This PR includes those changes.

Related issue(s)

Testing

• Checks pass

For a manual check, could run:

git clone https://github.com/nextstrain/rsv.git
cd rsv/ingest
git checkout curate/format-dates
nextstrain build . data/a/metadata.tsv

[joverlee521]

The switch over to the new augur curate commands look good to me!

I've left a comment for an alternative solution to the header lines issue, which is more "snakemake-y" and allows us to parallelize the rules.

[joverlee521]

Changes look good to me from inspection!

I triggered a trial run for the ingest and we can do a diff with the production data to make sure nothing has changed.

[joverlee521]

Trial run completed successfully and uploaded outputs to s3://nextstrain-data/files/workflows/rsv/trial/curate-format-dates/*. I compared the output metadata TSV files with the production files on S3 and there were no differences in the existing data, just a couple of new records for rsv/b that's been added since the last automated run.

Compared outputs with the current files with:

ingest/vendored/download-from-s3 s3://nextstrain-data/files/workflows/rsv/trial/curate-format-dates/a/metadata.tsv.gz ingest/data/test-run/a-metadata.tsv
ingest/vendored/download-from-s3 s3://nextstrain-data/files/workflows/rsv/a/metadata.tsv.gz ingest/data/a-metadata.tsv
daff diff ingest/data/a-metadata.tsv ingest/data/test-run/a-metadata.tsv > /tmp/rsv-a-metadata.tsv.diff

ingest/vendored/download-from-s3 s3://nextstrain-data/files/workflows/rsv/trial/curate-format-dates/b/metadata.tsv.gz ingest/data/test-run/b-metadata.tsv
ingest/vendored/download-from-s3 s3://nextstrain-data/files/workflows/rsv/b/metadata.tsv.gz ingest/data/b-metadata.tsv
daff diff ingest/data/b-metadata.tsv ingest/data/test-run/b-metadata.tsv > /tmp/rsv-b-metadata.tsv.diff