check_versions.yml

name: Check versions

on:
  workflow_dispatch:
  schedule:
    - cron: '30 4 * * TUE'

jobs:
  check:
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          lfs: true

      - name: Checkout LFS objects
        run: git lfs checkout
        
      - name: versions
        run: |
          issue_text="Needing updates:  " 
          workflow_containers=($(grep container modules/* | grep staphb | sort | uniq | grep -v latest | awk '{print $3}' | sed 's/'\''//g'))
          for container in ${workflow_containers[@]}
          do
            base=$(echo $container | cut -f 1 -d ":")
            workflow_version=$(echo $container | cut -f 2 -d ":")
            
            docker pull $base:latest
            latest_version=$(docker inspect --format '{{ index .Config.Labels "software.version"}}' $base:latest)
            
            if [[ "$latest_version" == "$workflow_version" ]]
            then
              echo "No version change for $base:$workflow_version" | tee -a versions.txt
            else
              echo "New version for $base! Upgrade to $latest_version from $workflow_version." | tee -a versions.txt
              issue_text="$issue_text<br>- $base from $workflow_version to $latest_version  "
            fi
          done

          latest_nextclade_version=$(docker run nextstrain/nextclade:latest nextclade --version | awk '{print $2}')
          worfklow_nextclade_version=$(grep container modules/nextclade.nf | cut -f 2 -d ":" | cut -f 1 -d "'" | head -n 1)

          if [[ "$latest_nextclade_version" == "$worfklow_nextclade_version" ]]
          then
            echo "No version change for nextstrain/nextclade:$worfklow_nextclade_version" | tee -a versions.txt
          else
            echo "New version for nextstrain/nextclade! Upgrade to $latest_nextclade_version from $worfklow_nextclade_version." | tee -a versions.txt
            issue_text="$issue_text<br>- nextstrain/nextclade from $worfklow_nextclade_version to $latest_nextclade_version  "
          fi

          latest_nextalign_version=$(docker run nextstrain/nextalign:latest nextalign --version | awk '{print $2}')
          worfklow_nextalign_version=$(grep container modules/nextalign.nf | cut -f 2 -d ":" | cut -f 1 -d "'" | head -n 1)

          if [[ "$latest_nextalign_version" == "$worfklow_nextalign_version" ]]
          then
            echo "No version change for nextstrain/nextalign:$worfklow_nextalign_version" | tee -a versions.txt
          else
            echo "New version for nextstrain/nextalign! Upgrade to $latest_nextalign_version from $worfklow_nextalign_version." | tee -a versions.txt
            issue_text="$issue_text<br>- nextstrain/nextalign from $worfklow_nextalign_version to $latest_nextalign_version  "
          fi

          echo $issue_text
          cat versions.txt
          echo 'ISSUE_TEXT='$issue_text >> $GITHUB_ENV
          
      - name: Create Issue
        run: |
          gh issue create --title "Version check" --body "$ISSUE_TEXT" --repo $GITHUB_REPOSITORY
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}