Template update for nf-core/tools version 2.3.1

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[*.{yml,yaml}]

[*.{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

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

[/modules/nf-core/**]

[/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:

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

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

    * 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

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)

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).

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.

: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`.

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

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

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

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

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

## Getting help

## Getting help

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

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

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

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`.

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`.

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

### Default values

### Default values

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

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

* initial process channel: `ch_output_from_<process>`

- initial process channel: `ch_output_from_<process>`

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

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

### Nextflow version bumping

### Nextflow version bumping

description: Report something that is broken or incorrect

description: Report something that is broken or incorrect

labels: bug

labels: bug

body:

body:

  - type: markdown

  - type: markdown

    attributes:

    attributes:

      value: |

      value: |

  - [ ] 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 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.

  - [ ] 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`).

- [ ] 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.

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

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

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

- [ ] `CHANGELOG.md` is updated.

- [ ] `CHANGELOG.md` is updated.

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

        # 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)

        # 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

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

        with:

        with:

          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}