Merge pull request #31 from luslab/dev

[*.{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`.

9. Do local tests that the new code works properly and as expected.

10. Add a new test command in `.github/workflow/ci.yaml`.

10. Add a new test command in `.github/workflow/ci.yml`.

11. If applicable add a [MultiQC](https://https://multiqc.info/) module.

12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.

13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.

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

I have checked the following places for your error:

- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)

- [ ] [nf-core/cutandrun pipeline documentation](https://nf-co.re/nf-core/cutandrun/usage)

- [ ] [nf-core/cutandrun pipeline documentation](https://nf-co.re/cutandrun/usage)

## Description of the bug

## Nextflow Installation

- Version: <!-- [e.g. 19.10.0] -->

- Version: <!-- [e.g. 21.04.0] -->

## Container engine

- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->

- version: <!-- [e.g. 1.0.0] -->

- Image tag: <!-- [e.g. nfcore/cutandrun:1.0.0] -->

## Additional context

- [ ] This comment contains a description of changes (with reason).

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

    - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`

    - [ ] 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.

- [ ] 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.