alignoth.github.io/.github/workflows/build_and_deploy.yml at main · alignoth/alignoth.github.io · GitHub

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name: build-and-deploy

on:
  schedule:
    - cron: '0 18 * * *'
  push:
    branches:
      - main
    workflow_dispatch:

permissions:
  contents: read
  pages: write
  id-token: write

jobs:
  build-and-deploy:
    environment:
      name: github-pages
      url: ${{ steps.deployment.outputs.page_url }}
    defaults:
      run:
        shell: bash -el {0}
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Install stable toolchain
        uses: actions-rs/toolchain@v1
        with:
            toolchain: stable

      - name: Install alignoth
        run: cargo install alignoth

      - name: Checkout alignoth repo
        uses: actions/checkout@v4
        with:
          repository: alignoth/alignoth
          path: alignoth

      - name: Build preview html
        run: alignoth -b alignoth/tests/sample_3/NA12878.bam -r alignoth/tests/sample_3/ref.fa -v alignoth/tests/sample_3/1257A.vcf.gz -g 1:250-500 --html --max-read-depth 40 > src/preview.html

      - name: locosopa
        uses: koesterlab/locosopa@main
        with:
          config: src/config.yaml
          path: build