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Arcadia-Science / metagenomics

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
MIT License
37 stars 2 forks source link

Process for downloading databases #18

Closed elizabethmcd closed 1 year ago

elizabethmcd commented 1 year ago

Figuring out best way to configure process for downloading databases vs just pointing to a path (S3 bucket). Default behavior should be downloading and can provide a parameter for a custom path locally or on S3. Figure this out with the sourmash databases for this workflow

elizabethmcd commented 1 year ago

For the sourmash databases - parameters or options to download specific ones - GTDB, Genbank (which lineages), the custom checkV one coming, etc.

elizabethmcd commented 1 year ago

check DBs don't download them, adds too many options for what we need, can add instructions for others to download the DBs separate from the workflow as preprep and then point to them