nextstrain-automation

Nextstrain automation

Note

External users can ignore this directory! This build config/customization is tailored for the internal Nextstrain team to extend the core ingest workflow for automated workflows.

Update the config

Update the config.yaml for your pathogen:

1. Edit the s3_dst param to add the pathogen repository name.
2. Edit the files_to_upload param to a mapping of files you need to upload for your pathogen. The default includes suggested files for uploading curated data and Nextclade outputs.

Run the workflow

Provide the additional config file to the Snakemake options in order to include the custom rules from upload.smk in the workflow. Specify the upload_all target in order to run the additional upload rules.

The upload rules will require AWS credentials for a user that has permissions to upload to the Nextstrain data bucket.

The customized workflow can be run from the top level pathogen repo directory with:

nextstrain build \
    --env AWS_ACCESS_KEY_ID \
    --env AWS_SECRET_ACCESS_KEY \
    ingest \
        upload_all \
        --configfile build-configs/nextstrain-automation/config.yaml

Automated GitHub Action workflows

Additional instructions on how to use this with the shared pathogen-repo-build GitHub Action workflow to come!