Hello,
Im trying to run the nf-core/metatdenovo pipeline and there are several databases that can be use.
For the program diamond you have to provide a .csv file with this structure:
db,dmnd_path,taxdump_names,taxdump_nodes,ranks,parse_with_taxdump
gtdb,diamond-taxonomy/gtdb_r220_repr.dmnd,diamond-taxonomy/gtdb_taxdump/names.dmp,diamond-taxonomy/gtdb_taxdump/nodes.dmp,domain;phylum;class;order;genus;species;strain,
refseq,diamond-taxonomy/refseq_protein.taxonomy.dmnd,diamond-taxonomy/ncbi_taxdump/names.dmp,diamond-taxonomy/ncbi_taxdump/nodes.dmp,,true
I've try to search for the databases in the /share/bank but I didn't find them. Could someone tell me if the GTDB database to use with diamond is already made somewhere? If not the creators of the pipeline provide this Figshare link to download it directly but I haven't found a way to do directly to the cluster. Does anyone knows how to download files from figshare directly to the cluster?
Thank you,
Carla.