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TYMichaelsen / covid19

Bioinformatic pipelines used to assemble SARS-CoV-2 genomes from DK
GNU General Public License v3.0
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Microreact integration #47

Open MiroPakanec opened 4 years ago

MiroPakanec commented 4 years ago

in bi_systems/microreact_pipeline there are 2 main scripts:

  1. main_micororeact.py

    • args: path to config (use bi_systems/microreact_pipeline/config/microreact.json) date - you can specify nextstrain date (default is latest - finds the most recent) date_folder_suffix - default 'nextstrain' (specify only if folder name diviates from standard)
    • description: fetches latest metadata and tree files, preprocesses them and uploadest them to google drive (microreact gets updated).

  2. main_website.py

    • args: path to config (use bi_systems/microreact_pipeline/config/web.json)
    • description: uploads latest stats (displayed on the front page)
    • additionally, computes and uploads statistics data, but this was disabled on the website