Merge remote-tracking branch 'nf-core/nf-core-template-merge-2.2' into template_merge

1. Define the corresponding input channel into your new process from the expected previous process channel

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`).

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.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`.

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

5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).

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.

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

### Default values

If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`

### Software version reporting

If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.

Add to the script block of the process, something like the following:

```bash

<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true

```

or

```bash

<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true

```

You then need to edit the script `bin/scrape_software_versions.py` to:

1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`

2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.

### Images and figures

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

---

name: Bug report

about: Report something that is broken or incorrect

labels: bug

---

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# nf-core/cutandrun bug report

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Please delete this text and anything that's not relevant from the template below:

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## Check Documentation

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/cutandrun/usage)

## Description of the bug

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## Nextflow Installation

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## Additional context

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name: Bug report

description: Report something that is broken or incorrect

labels: bug

body:

  - type: markdown

    attributes:

      value: |

        Before you post this issue, please check the documentation:

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

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

  - type: textarea

    id: description

    attributes:

      label: Description of the bug

      description: A clear and concise description of what the bug is.

    validations:

      required: true

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    id: command_used

    attributes:

      label: Command used and terminal output

      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.

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        $ nextflow run ...

        Some output where something broke

  - type: textarea

    id: files

    attributes:

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      description: |

        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.

        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.

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    id: system

    attributes:

      label: System information

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        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

        * OS _(eg. CentOS Linux, macOS, Linux Mint)_

        * Version of nf-core/cutandrun _(eg. 1.1, 1.5, 1.8.2)_

blank_issues_enabled: false

contact_links:

  - name: Join nf-core

    url: https://nf-co.re/join

---

name: Feature request

about: Suggest an idea for the nf-core/cutandrun pipeline

labels: enhancement

---

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# nf-core/cutandrun feature request

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Please delete this text and anything that's not relevant from the template below:

-->

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