There should be a way to pre-download all of the present genomes from NCBI so that YAVSAP can be run offline.
Added Features
Additional parameters
Propose any new parameters that would be needed to implement this feature,
including its name, type, and default value, and explain how it would be
consumed by the new/existing processes.
--download_genomes
Switches the pipeline to "genome download" mode, where it will not run any analysis, but will instead simply download and reformat the reference genome files from NCBI.
Additional output
Reference genome fasta/GenBank file corresponding to --genome
Strain reference genome fasta/GenBank file containing all of the sequences from --genome_list
Strain reference genome TSV file that points to 2 in a format YAVSAP can recognize (i.e., from #44, /data/yavsap/results/genomes.fasta:NC_01234.1).
These files should probably be output even if downloading the files directly in the pipeline (the way it's done now).
Summary
There should be a way to pre-download all of the present genomes from NCBI so that YAVSAP can be run offline.
Added Features
Additional parameters
--download_genomesAdditional output
--genome--genome_list/data/yavsap/results/genomes.fasta:NC_01234.1).These files should probably be output even if downloading the files directly in the pipeline (the way it's done now).