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: Check pipeline names and add missing configs
        id: check-pipelines
        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

            echo "changed=true" >> $GITHUB_OUTPUT
            fi
          done

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

      - name: Commit & push changes
        id: commit-and-push
        if: steps.check-pipelines.outputs.changed == 'true'
        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
        if: steps.check-pipelines.outputs.changed == 'true'
        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
          reviewers: |
            "mashehu"
            "jfy133"
            "maxulysse"