build-cutadapt.yml

name: Cutadapt CI

# Controls when the workflow will run.
on:
  # Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
  pull_request:
    branches: [ "develop", "master" ]
    paths:
      - '3rd-party-tools/cutadapt/**'
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:
    inputs:
      image_tag:
        description: 'Docker Image Tag (default: branch_name)' 

env:
  PROJECT_NAME: WARP 3rd Party Tools
  # Github repo name
  REPOSITORY_NAME: ${{ github.event.repository.name }}
  # Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
  DOCKER_REGISTRY: us.gcr.io
  GCR_PATH: broad-gotc-prod/cutadapt
  ACR_PATH: cutadapt
  TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}

  # A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # The job that builds our container
  build-for-gcr:
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: 3rd-party-tools/cutadapt
    # Map a step output to a job output
    outputs:
      imagePath: ${{ steps.saveImagePath.outputs.url }}
    steps:
    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
    - uses: actions/checkout@v3
    - name: Build the Docker image
      run: docker build . --file Dockerfile --tag ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}
    - name: Check working directory'
      run: |
        echo "Current directory: "
        pwd
        ls -lht
    # Save the image path to an output
    - id: 'saveImagePath'
      run: echo "url=${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}" >> $GITHUB_OUTPUT
    # Log into the Google Docker registry
    - id: 'Auth'
      name: Login to GCR
      uses: docker/login-action@v2
      with:
        registry: ${{ env.DOCKER_REGISTRY }}
        username: _json_key
        password: ${{ secrets.GCR_CI_KEY }}
    # Push the image to the Google Docker registry
    - name: Push image
      run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"

  build-for-acr:
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: 3rd-party-tools/cutadapt
    steps:
    # checkout the repo
    - name: 'Checkout GitHub Action'
      uses: actions/checkout@v3
      
    - name: 'Login via Azure CLI'
      uses: azure/login@v1
      with:
        creds: ${{ secrets.AZURE_CREDENTIALS }}
    
    - name: 'Build and push image'
      uses: azure/docker-login@v1
      with:
        login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
        username: ${{ secrets.REGISTRY_USERNAME }}
        password: ${{ secrets.REGISTRY_PASSWORD }}
    - run: |
        docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
        docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}