update-pipeline-configs.yml

name: Update Pipeline Configs
on:
  schedule:
    - cron: '0 0 * * *' # Run every day at midnight
  workflow_dispatch:


jobs:
  update_configs:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Fetch pipeline names
        run: |
          curl -o pipeline_names.json https://nf-co.re/pipeline_names.json

      - name: add test pipeline to pipeline_names.json #TODO remove this testing step after successful tests
        run: |
          jq '.pipeline += ["test"]' pipeline_names.json > tmp.json
          mv tmp.json pipeline_names.json

      - name: Check pipeline names and add missing configs
        run: |
            pipeline=$(jq -r '.pipeline[]' pipeline_names.json)
            for pipeline in $pipeline; do
              printf "Checking pipeline: %s\n" $pipeline
              if [ ! -f "pipeline/${pipeline}.config" ]; then
                cat << EOF > "pipeline/${pipeline}.config"
            /*
            * -------------------------------------------------
            *  nfcore/${pipeline} custom profile Nextflow config file
            * -------------------------------------------------
            * Config options for custom environments.
            * Cluster-specific config options should be saved
            * in the conf/pipeline/${pipeline} folder and imported
            * under a profile name here.
            */

            profiles {
            }
            EOF
              fi
            done

      - name: inspect test pipeline config #TODO remove this testing step after successful tests
        run: |
          cat pipeline/test.config

      - name: clean up
        run: |
          rm pipeline_names.json

      - name: Commit & push changes
        id: commit-and-push
        run: |
          git config user.email "core@nf-co.re"
          git config user.name "nf-core-bot"
          git add .
          git status
          git commit -m "[automated] Update pipeline configs"

      - name: Create PR
        uses: peter-evans/create-pull-request@70a41aba780001da0a30141984ae2a0c95d8704e # v6
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          commit-message: Update pipeline configs
          title: Update pipeline configs
          body: |
            This is an automated PR to update pipeline configs for newly created nf-core pipelines.
          branch: 'update-pipeline-configs-'${{ github.run_id }}
          delete-branch: true
          base: 'master'
          draft: false