Merge branch 'chris-feat' into dev

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[*.{md,yml,yaml,html,css,scss,js}]

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[*.json]

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# These files are edited and tested upstream in nf-core/modules

[/modules/nf-core/**]

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If you'd like to write some code for nf-core/cutandrun, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the [nf-core/cutandrun issues](https://github.com/nf-core/cutandrun/issues) to avoid duplicating work

    * If there isn't one already, please create one so that others know you're working on this

1. Check that there isn't already an issue about your idea in the [nf-core/cutandrun issues](https://github.com/nf-core/cutandrun/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this

2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/cutandrun repository](https://github.com/nf-core/cutandrun) to your GitHub account

3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)

4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).

:warning: Only in the unlikely and regretful event of a release happening with a bug.

* On your own fork, make a new branch `patch` based on `upstream/master`.

* Fix the bug, and bump version (X.Y.Z+1).

* A PR should be made on `master` from patch to directly this particular bug.

- On your own fork, make a new branch `patch` based on `upstream/master`.

- Fix the bug, and bump version (X.Y.Z+1).

- A PR should be made on `master` from patch to directly this particular bug.

## Getting help

6. Add sanity checks and validation for all relevant parameters.

7. Perform local tests to validate that the new code works as expected.

8. If applicable, add a new test command in `.github/workflow/ci.yml`.

9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.

9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.

10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.

### Default values

Please use the following naming schemes, to make it easy to understand what is going where.

* initial process channel: `ch_output_from_<process>`

* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`

- initial process channel: `ch_output_from_<process>`

- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`

### Nextflow version bumping

description: Report something that is broken or incorrect

labels: bug

body:

  - type: markdown

    attributes:

      value: |

Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)

-->

<!-- markdownlint-disable ul-indent -->

## PR checklist

  - [ ] 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` --outdir <OUTDIR>`).

- [ ] 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.

        # 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 }}

          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}

          pipeline: ${{ github.repository }}

          revision: ${{ github.sha }}

          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/cutandrun/work-${{ github.sha }}

          parameters: |

            {