Genome metadata QC filtering

[epbrenner]

Adding new functionality.

1. .parse_bvbrc_tsv() is a helper to more safely merge TSV data from parallel workers after I noticed a tab shift in data somewhere yielded strain names in the accession ID column and such after a failed merge.
2. .apply_metadata_qc is the big one, which allows you to screen BV-BRC genome metadata for CheckM completeness and CheckM contamination values. By default, I set these values very loose at 90% complete and 10% contamination being the cutoffs. We can adjust as needed. Additionally, you can enable filters based on CDS counts, genome length, and GC content, which are set based on deviations away from the median value of the distribution of those values for the input taxon. This will not work well for multi-taxon bug sets so this is set to NULL by default!
3. Updated the retrieveMetadata() and prepareGenomes() functions to accept the apply_metadata_qc steps.
4. Updated .ftpes_download_one to incorporate the old .is_complete helper inside the loop. This avoids a BiocParallel issue where the workers did not inherit the helpers.
5. Updated a spot where an old ftp_download_one function was called instead of ftpes_download_one

@amcim Most importantly for you, I know you've been working on the BiocParallel stuff and had since moved on to another implementation (futures?). I just want to confirm that this script is working for me locally after my patches, but this is just based off main. If we're changing implementations, some of my updates aren't necessary.

For testers:
Open GitHub Desktop or your preferred method of fetching a PR, fetch this PR, source data_curation.R into your favorite CLI, and try retrieveMetadata(user_bacs = "Shigella flexneri") for a quick bug, or prepareGenomes(user_bacs = "Shigella flexneri") to also test the genome downloader. I have tried this out locally for Enterobacter spp., K. pnumoniae, and Campylobacter jejuni. Give it a spin!