Update Pipeline Configs #51
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| 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" |