fetch-and-ingest-gisaid-branch.yml

name: GISAID fetch and ingest (on branch)

# Manually triggered using GitHub's UI
on: workflow_dispatch

jobs:
  ingest:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
    - uses: nextstrain/.github/actions/setup-nextstrain-cli@master

    - name: run_pipeline
      run: |
        ./bin/write-envdir env.d \
          AWS_DEFAULT_REGION \
          GISAID_API_ENDPOINT \
          GISAID_USERNAME_AND_PASSWORD \
          GITHUB_RUN_ID \

        GITHUB_BRANCH=${GITHUB_REF#refs/heads/}
        declare -a config
        config+=(
          fetch_from_database=True
          s3_dst=s3://nextstrain-ncov-private/branch/"${GITHUB_BRANCH}"
        )

        nextstrain build \
          --aws-batch \
          --detach \
          --no-download \
          --image nextstrain/ncov-ingest \
          --cpus 16 \
          --memory 68GiB \
          --exec env \
          . \
            envdir env.d snakemake \
              --configfile config/gisaid.yaml \
              --config "${config[@]}" \
              --cores 16 \
              --resources mem_mb=68000 \
              --printshellcmds
      env:
        AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
        GISAID_API_ENDPOINT: ${{ secrets.GISAID_API_ENDPOINT }}
        GISAID_USERNAME_AND_PASSWORD: ${{ secrets.GISAID_USERNAME_AND_PASSWORD }}
        GITHUB_RUN_ID: ${{ github.run_id }}
        GITHUB_REF: ${{ github.ref }}