Add dummy configs for all missing configs #1
Workflow file for this run
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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: 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 "[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 | ||
| 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 | ||
