Update Pipeline Configs #206
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 "[email protected]" | |
| 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" |