Template update for nf-core/tools version 2.1

[*.{yml,yaml}]

indent_size = 2

[*.json]

insert_final_newline = unset

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

[/modules/nf-core/**]

charset = unset

    * 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).

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).

5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).

2. Write the process block (see below).

3. Define the output channel if needed (see below).

4. Add any new flags/options to `nextflow.config` with a default (see below).

5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).

5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).

6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).

7. Add sanity checks for all relevant parameters.

8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.

Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.

Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.

Once there, use `nf-core schema build` to add to `nextflow_schema.json`.

### Default processes resource requirements

- [ ] If you've fixed a bug or added code that should be tested, add tests!

    - [ ] 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 .`).

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

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

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

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

      - uses: actions/setup-node@v1

        with:

          node-version: "10"

          node-version: '10'

      - name: Install editorconfig-checker

        run: npm install -g editorconfig-checker

## Quick Start

1. Install [`Nextflow`](https://nf-co.re/usage/installation) (`>=21.04.0`)

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`)

2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_