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COG-UK / datapipe

Nextflow implementation of grapevine
GNU General Public License v3.0
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GISAID JSON DUMP #39

Open leke-lyu opened 11 months ago

leke-lyu commented 11 months ago

Hi there, Really excited to know this tool! Want to apply this pipeline to precess global contextual data from GISAID. Question: How to prepare JSON dump from GISAID?

rmcolq commented 11 months ago

You will need to communicate directly with GISAID to request bulk download credentials, letting them know what you plan to use it for. Once you have credentials, let me know if the bulk download has changed format - GISAID have changed how users download data several times over the last few years and it is outside of our control what they provide.

leke-lyu commented 11 months ago

Thanks, that helps a lot. Could you include some example datasets in the pipeline? These datasets won't be large, making it easier for users to run test runs and familiarize themselves with the process.