Is your feature request related to a problem? Please describe.
Whenever QUAST is run and reference genomes are not provided it will try to identify some references and fetch them from NCBI. Since all of those are saved to a temporary directory, they will be removed after the action completes.
Describe the solution you'd like
It would be great if we could collect those genomes and output them as GenomeData[DNASequence] artifact - that way, next time when a user wants to re-run QUAST for whatever reason, they can just pass those references instead of re-downloading all of them.
Additional context
The references fetched by QUAST are combined into a single file which can be found in results/quast_downloaded_references (?). Alternatively, individual references could also be passed - not sure what kind of artifact they should be stored in, though.
Is your feature request related to a problem? Please describe. Whenever QUAST is run and reference genomes are not provided it will try to identify some references and fetch them from NCBI. Since all of those are saved to a temporary directory, they will be removed after the action completes.
Describe the solution you'd like It would be great if we could collect those genomes and output them as
GenomeData[DNASequence]artifact - that way, next time when a user wants to re-run QUAST for whatever reason, they can just pass those references instead of re-downloading all of them.Additional context The references fetched by QUAST are combined into a single file which can be found in
results/quast_downloaded_references(?). Alternatively, individual references could also be passed - not sure what kind of artifact they should be stored in, though.