create-test-lint-wf-template.yml

name: Create a pipeline from a template and test it
on:
  push:
    branches:
      - dev
      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
      - "renovate/**" # branches Renovate creates
    paths:
      - nf_core/pipeline-template/**
  pull_request:
    paths-ignore:
      - "docs/**"
      - "CHANGELOG.md"
  release:
    types: [published]
  workflow_dispatch:

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  NXF_ANSI_LOG: false
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

jobs:
  prepare-matrix:
    name: Retrieve all template features
    runs-on: ubuntu-latest
    outputs:
      all_features: ${{ steps.create_matrix.outputs.matrix }}
    steps:
      - name: checkout
        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
      - name: Create Matrix
        id: create_matrix
        run: |
          echo "matrix=$(yq '.[].features | keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config")' nf_core/pipelines/create/template_features.yml | \
          yq 'flatten | tojson(0)' -)" >> $GITHUB_OUTPUT

  RunTestWorkflow:
    runs-on:
      - runs-on=${{ github.run_id }}-run-test-worfklow
      - runner=4cpu-linux-x64
    needs: prepare-matrix
    env:
      NXF_ANSI_LOG: false

    strategy:
      matrix:
        TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
        include:
          - TEMPLATE: all
      fail-fast: false

    steps:
      - name: Check out source-code repository
        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

      - name: Set up Python 3.13
        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
        with:
          python-version: "3.13"

      - name: Install python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install .

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: latest-everything

      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1
        with:
          version: "0.9.2"
          install-pdiff: true

      # Create template files
      - name: Create template skip ${{ matrix.TEMPLATE }}
        run: |
          mkdir create-test-lint-wf
          export NXF_WORK=$(pwd)
          if [ ${{ matrix.TEMPLATE }} == "all" ]
          then
            printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
          else
            printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml
          fi

      # Create a pipeline from the template
      - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
        run: |
          cd create-test-lint-wf
          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml

      # Copy snapshot file
      - name: copy snapshot file
        if: ${{ matrix.TEMPLATE  != 'all' && matrix.TEMPLATE != 'nf-test' }}
        run: |
          if [ ! -f ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap ]; then
              echo "Generate a snapshot when creating a pipeline and skipping the feature ${{ matrix.TEMPLATE }}."
              echo "Then, copy it to the directory .github/snapshots"
          else
            cp ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap
          fi

      # Run pipeline with nf-test
      - name: run pipeline nf-test
        if: ${{ matrix.TEMPLATE  != 'all' && matrix.TEMPLATE != 'nf-test' }}
        shell: bash
        run: |
          cd create-test-lint-wf/my-prefix-testpipeline
          nf-test test \
            --profile=+docker \
            --verbose \
            --ci

      # Remove .nf-test folder before linting
      - name: remove .nf-test folder
        if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }}
        run: |
          rm -rf create-test-lint-wf/my-prefix-testpipeline/.nf-test
          rm create-test-lint-wf/my-prefix-testpipeline/.nf-test.log
          rm create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap

      # Run the pipeline when nf-test is not available
      - name: run the pipeline
        if: ${{ matrix.TEMPLATE == 'all' || matrix.TEMPLATE == 'nf-test' }}
        run: |
          cd create-test-lint-wf
          nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results

      # Remove results folder before linting
      - name: remove results folder
        if: ${{ matrix.TEMPLATE == 'all' || matrix.TEMPLATE == 'nf-test' }}
        run: |
          rm -rf create-test-lint-wf/results

      # Try syncing it before we change anything
      - name: nf-core pipelines sync
        run: nf-core --log-file log.txt pipelines sync --dir create-test-lint-wf/my-prefix-testpipeline/

      # Run code style linting
      - name: Run pre-commit
        run: pre-commit run --all-files
        working-directory: create-test-lint-wf

      # Remove TODO statements
      - name: remove TODO
        run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
        working-directory: create-test-lint-wf

      # Uncomment includeConfig statement
      - name: uncomment include config
        run: find my-prefix-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
        working-directory: create-test-lint-wf

      # Replace zenodo.XXXXXX to pass readme linting
      - name: replace zenodo.XXXXXX
        run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
        working-directory: create-test-lint-wf

      # Add empty ro-crate file
      - name: add empty ro-crate file
        run: touch my-prefix-testpipeline/ro-crate-metadata.json
        working-directory: create-test-lint-wf

      # Run nf-core linting
      - name: nf-core pipelines lint
        run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned
        working-directory: create-test-lint-wf

      # Run code style linting
      - name: run pre-commit
        shell: bash
        run: pre-commit run --all-files
        working-directory: create-test-lint-wf

      # Run bump-version
      - name: nf-core pipelines bump-version
        run: nf-core --log-file log.txt pipelines bump-version --dir my-prefix-testpipeline/ 1.1
        working-directory: create-test-lint-wf

      # Run nf-core linting in release mode
      - name: nf-core pipelines lint in release mode
        run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned --release
        working-directory: create-test-lint-wf

      - name: Tar files
        run: tar -cvf artifact_files.tar log.txt template_skip*.yml
        working-directory: create-test-lint-wf

      - name: Upload log file artifact
        if: ${{ always() }}
        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
        with:
          name: nf-core-log-file-${{ matrix.TEMPLATE }}
          path: create-test-lint-wf/artifact_files.tar

      - name: Cleanup work directory
        run: sudo rm -rf create-test-lint-wf
        if: always()