Template update for nf-core/tools version 1.13.2

    strategy:

      matrix:

        # Nextflow versions: check pipeline minimum and current latest

        nxf_ver: ['20.04.0', '']

        nxf_ver: ['20.04.0', '21.03.0-edge']

    steps:

      - name: Check out pipeline code

        uses: actions/checkout@v2

        run: npm install -g markdownlint-cli

      - name: Run Markdownlint

        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml

      # If the above check failed, post a comment on the PR explaining the failure

      - name: Post PR comment

        if: failure()

        uses: mshick/add-pr-comment@v1

        with:

          message: |

            ## Markdown linting is failing

            To keep the code consistent with lots of contributors, we run automated code consistency checks.

            To fix this CI test, please run:

            * Install `markdownlint-cli`

                * On Mac: `brew install markdownlint-cli`

                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)

            * Fix the markdown errors

                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`

                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`

            Once you push these changes the test should pass, and you can hide this comment :+1:

            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

            Thanks again for your contribution!

          repo-token: ${{ secrets.GITHUB_TOKEN }}

          allow-repeats: false

  YAML:

    runs-on: ubuntu-latest

    steps:

      - name: Install yaml-lint

        run: npm install -g yaml-lint

      - name: Run yaml-lint

        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")

        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")

      # If the above check failed, post a comment on the PR explaining the failure

      - name: Post PR comment

        if: failure()

        uses: mshick/add-pr-comment@v1

        with:

          message: |

            ## YAML linting is failing

            To keep the code consistent with lots of contributors, we run automated code consistency checks.

            To fix this CI test, please run:

            * Install `yaml-lint`

                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)

            * Fix the markdown errors

                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`

                * Fix any reported errors in your YAML files

            Once you push these changes the test should pass, and you can hide this comment :+1:

            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

            Thanks again for your contribution!

          repo-token: ${{ secrets.GITHUB_TOKEN }}

          allow-repeats: false

  nf-core:

    runs-on: ubuntu-latest

    steps:

FROM nfcore/base:1.13.1

FROM nfcore/base:1.13.2

LABEL authors="Chris Cheshire and Charlotte West" \

      description="Docker image containing all software requirements for the nf-core/cutandrun pipeline"