config.yaml

# This configuration file should contain all required configuration parameters
# for the ingest workflow to run with additional Nextstrain automation rules.

# Custom rules to run as part of the Nextstrain automated workflow
# The paths should be relative to the ingest directory.
custom_rules:
  - build-configs/nextstrain-automation/upload.smk

# Nextstrain CloudFront domain to ensure that we invalidate CloudFront after the S3 uploads
# This is required as long as we are using the AWS CLI for uploads
cloudfront_domain: "data.nextstrain.org"

# Nextstrain AWS S3 Bucket with pathogen prefix
# Replace <pathogen> with the pathogen repo name.
s3_dst: "s3://nextstrain-data/files/workflows/oropouche"

# Mapping of files to upload.
# Keys here are the target S3 key (after combining with "s3_dst")
# Values are the local files produced by the workflow
files_to_upload:
  ncbi.ndjson.zst: data/ncbi.ndjson
  metadata.tsv.zst: results/metadata.tsv
  L/sequences.fasta.zst: results/L/sequences.fasta
  M/sequences.fasta.zst: results/M/sequences.fasta
  S/sequences.fasta.zst: results/S/sequences.fasta