Merge branch 'chris-feat' into dev

name: Bug report

description: Report something that is broken or incorrect

labels: bug

    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)

    - [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.

- [ ] Make sure your code lints (`nf-core lint`).

- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).

- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).

- [ ] Usage Documentation in `docs/usage.md` is updated.

- [ ] Output Documentation in `docs/output.md` is updated.

- [ ] `CHANGELOG.md` is updated.

    runs-on: ubuntu-latest

    steps:

      - name: Launch workflow via tower

        uses: nf-core/tower-action@v2

        uses: nf-core/tower-action@v3

        # TODO nf-core: You can customise AWS full pipeline tests as required

        # Add full size test data (but still relatively small datasets for few samples)

        # on the `test_full.config` test runs with only one set of parameters

        with:

          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"

            }

          profiles: test_full,aws_tower

          pre_run_script: 'export NXF_VER=21.10.3'

          nextflow_config: |

            process.errorStrategy = 'retry'

            process.maxRetries = 3

    runs-on: ubuntu-latest

    steps:

      - name: Launch workflow via tower

        uses: nf-core/tower-action@v2

        uses: nf-core/tower-action@v3

        with:

          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-test-${{ github.sha }}"

            }

          profiles: test,aws_tower

          pre_run_script: 'export NXF_VER=21.10.3'

          nextflow_config: |

            process.errorStrategy = 'retry'

            process.maxRetries = 3

    runs-on: ubuntu-latest

    steps:

      - uses: actions/checkout@v2

      - uses: actions/setup-node@v1

        with:

          node-version: '10'

      - uses: actions/setup-node@v2

      - name: Install markdownlint

        run: npm install -g markdownlint-cli

      - name: Run Markdownlint

    steps:

      - uses: actions/checkout@v2

      - uses: actions/setup-node@v1

        with:

          node-version: '10'

      - uses: actions/setup-node@v2

      - name: Install editorconfig-checker

        run: npm install -g editorconfig-checker

  YAML:

    runs-on: ubuntu-latest

    steps:

      - uses: actions/checkout@v1

      - uses: actions/setup-node@v1

      - name: Checkout

        uses: actions/checkout@master

      - name: 'Yamllint'

        uses: karancode/yamllint-github-action@master

        with:

          node-version: '10'

      - name: Install yaml-lint

        run: npm install -g yaml-lint

      - name: Run yaml-lint

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

          yamllint_file_or_dir: '.'

          yamllint_config_filepath: '.yamllint.yml'

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

      - name: Post PR comment

            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`)

            * Install `yamllint`

                * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint)

                instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint)

            * Fix the markdown errors

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

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

                * Fix any reported errors in your YAML files

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