Locate fastq data associated with MGnify analyses

[s-meaden]

Adding this as an issue in case anyone has a similar problem.

MGnifyR::get_download_urls() doesn't return links for the read data (fastq) used to generate assemblies/analyses, but this may be useful for some scenarios.

A workaround is to run MGnifyR::mgnify_get_analyses_metadata() then use the ENA accessions returned under the sample_biosample column.

These accessions can be used with the enaGroupGet command from the enaBrowserTools scripts, e.g.: enaGroupGet -f fastq SAMN04360062

Note that the enaDataGet throws an error and doesn't find the accession (for me at least).

Thanks @beadyallen for the package!

[TuomasBorman]

TODO:

1. Check if raw sequences can be found from MGnify (@SandyRogers do you have direct answer for this?)
2. If they cannot be found, consider adding a method that gets these files from ENA.