create-test-lint-wf-template.yml

name: Create a pipeline from a template and test it
on:
  push:
    branches:
      - dev
    paths:
      - nf_core/pipeline-template/**
  pull_request:
  release:
    types: [published]

# 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:
  RunTestWorkflow:
    runs-on: ${{ matrix.runner }}
    env:
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        TEMPLATE:
          - "template_skip_github_badges.yml"
          - "template_skip_igenomes.yml"
          - "template_skip_ci.yml"
        runner: ["self-hosted"]
        profile: ["self_hosted_runner"]
        include:
          - TEMPLATE: "template_skip_all.yml"
            runner: ubuntu-latest
            profile: "docker"
          - TEMPLATE: "template_skip_nf_core_configs.yml"
            runner: ubuntu-latest
            profile: "docker"
      fail-fast: false

    steps:
      - name: go to working directory
        run: |
          mkdir -p create-lint-wf-template
          cd create-lint-wf-template
          export NXF_WORK=$(pwd)

      - uses: actions/checkout@v4
        name: Check out source-code repository

      - name: Set up Python 3.11
        uses: actions/setup-python@v5
        with:
          python-version: 3.11

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

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: latest-everything

      # Create template files
      - name: Create template skip all (except github)
        run: |
          mkdir create-test-lint-wf
          export NXF_WORK=$(pwd)
          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml

      - name: Create template skip github_badges
        run: |
          printf "prefix: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml

      - name: Create template skip igenomes
        run: |
          printf "prefix: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml

      - name: Create template skip ci
        run: |
          printf "prefix: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml

      - name: Create template skip nf_core_configs
        run: |
          printf "prefix: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml

      # 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 create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}

      - name: run the pipeline
        run: |
          cd create-test-lint-wf
          nextflow run my-prefix-testpipeline -profile test,${{matrix.profile}} --outdir ./results

      # Remove results folder before linting
      - name: remove results folder
        run: |
          rm -rf create-test-lint-wf/results

      # Try syncing it before we change anything
      - name: nf-core sync
        run: nf-core --log-file log.txt 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

      # 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

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

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

      # Run nf-core linting in release mode
      - name: nf-core lint in release mode
        run: nf-core --log-file log.txt --hide-progress 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: ${{ always() }}
        uses: actions/upload-artifact@v4
        with:
          name: nf-core-log-file-${{ matrix.TEMPLATE }}
          path: create-test-lint-wf/artifact_files.tar

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