Update Nextclade version and default datasets

[jpalmer37]

Fixes: https://github.com/BCCDC-PHL/fluviewer-nf/issues/30

[jpalmer37]

The --reference parameter within the nextclade dataset get command has been deprecated and throws an error:

Error: 
   0: The argument `--reference` (alias `-r`) is removed.

      Nextclade datasets are now identified only by their name (`--name`) and, optionally, a version tag (`--tag`). All other attributes are now included into the name.

      In order to list all dataset names, type:

        nextclade dataset list --names-only

      For more information, type

        nextclade dataset get --help

      Read Nextclade documentation at:

        https://docs.nextstrain.org/projects/nextclade/en/stable

Location:
   packages/nextclade-cli/src/cli/nextclade_cli.rs:1076

I will update this command accordingly.

[jpalmer37]

It appears that there has also been an update to the nextclade run interface:

  -P, --output-translations <OUTPUT_TRANSLATIONS>
          Template string for path to output fasta files containing translated and aligned peptides. A separate file will be generated for every gene.

          The string should contain template variable `{cds}`, where the gene name will be substituted. Make sure you properly quote and/or escape the curly braces, so that your shell, programming language or pipeline manager does not attempt to substitute the variables.

          Takes precedence over paths configured with `--output-all`, `--output-basename` and `--output-selection`.

          If the provided file path ends with one of the supported extensions: "gz", "bz2", "xz", "zst", then the file will be written compressed. Use "-" to write the uncompressed to standard output (stdout).

          If the required directory tree does not exist, it will be created.

          Example for bash shell:

          --output-translations='output_dir/nextclade.cds_translation.{cds}.fasta'

It now uses the template variable {cds} instead of {gene}. Will update accordingly.