datasets icon indicating copy to clipboard operation
datasets copied to clipboard

Add an `--include all` option to `datasets download genome`

Open dtdoering opened this issue 8 months ago • 2 comments

Is your feature request related to a problem? Please describe.

In my workflow, I frequently want to get the latest genome/annotation files for a number of RefSeq (GCF_*) and GenBank (GCA_*) genomes to do some further analyses. However, it can be hard to remember the exact spelling/terms used for each of the options, particularly when each desired file has to be listed.

Describe the solution you'd like

As a QoL feature, I'd like to be able to save some keystrokes by typing e.g.:

datasets download genome accession GCA_005981935.1 --include all

instead of:

datasets download genome accession GCA_005981935.1 --include genome,protein,cds,gff3,gbff,seq-report

So that the only thing I need to remember or copy/paste is the accession, instead of the accession and then the files listing.

Thanks!

dtdoering avatar Jun 10 '24 20:06 dtdoering