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).
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 thesample_biosamplecolumn.These accessions can be used with the enaGroupGet command from the enaBrowserTools scripts, e.g.:
enaGroupGet -f fastq SAMN04360062Note that the enaDataGet throws an error and doesn't find the accession (for me at least).
Thanks @beadyallen for the package!