rebuild-100k.yml

name: Rebuild 100k sample

on:
  # cron job once a week on Mondays at 12:42 UTC
  schedule:
    - cron:  '42 12 * * 1'
  # Manually triggered using GitHub's UI
  workflow_dispatch:

jobs:
  gisaid:
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      runtime: aws-batch
      run: |
        set -x

        declare -a config
        config+=(slack_token=$SLACK_TOKEN)

        nextstrain build \
          --detach \
          --cpus 16 \
          --memory 31GiB \
          . \
            upload \
            --configfile nextstrain_profiles/100k/config-gisaid.yaml \
            --config "${config[@]}" \
            --set-threads tree=8
      artifact-name: gisaid-build-output

  open:
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      runtime: aws-batch
      run: |
        set -x

        declare -a config
        config+=(slack_token=$SLACK_TOKEN)

        nextstrain build \
          --detach \
          --cpus 16 \
          --memory 31GiB \
          . \
            upload \
            --configfile nextstrain_profiles/100k/config-open.yaml \
            --config "${config[@]}" \
            --set-threads tree=8
      artifact-name: open-build-output