Template update for nf-core/tools version 1.14

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

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

## PR checklist

- [ ] 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 .`).

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

  release:

    types: [published]

# Uncomment if we need an edge release of Nextflow again

# env: NXF_EDGE: 1

jobs:

  test:

    name: Run workflow tests

    strategy:

      matrix:

        # Nextflow versions: check pipeline minimum and current latest

        nxf_ver: ['20.04.0', '21.03.0-edge']

        nxf_ver: ['20.04.0', '']

    steps:

      - name: Check out pipeline code

        uses: actions/checkout@v2

FROM nfcore/base:1.13.3

FROM nfcore/base:1.14

LABEL authors="Chris Cheshire and Charlotte West" \

      description="Docker image containing all software requirements for the nf-core/cutandrun pipeline"

## Quick Start

1. Install [`nextflow`](https://nf-co.re/usage/installation)

1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.04.0`)

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))_

            }

            // unexpected params

            def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'

            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam)) {

            def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }

            def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()

            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !expectedParamsLowerCase.contains(specifiedParamLowerCase)) {

                // Temporarily remove camelCase/camel-case params #1035

                def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}

                if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){

                    unexpectedParams.push(specifiedParam)

                }

            }

        }

        //=====================================================================//

        // Validate parameters against the schema

            }

            // Cast Duration to String

            if (p['value'].getClass() == nextflow.util.Duration) {

                new_params.replace(p.key, p['value'].toString())

                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))

            }

            // Cast LinkedHashMap to String

            if (p['value'].getClass() == LinkedHashMap) {

        }

        workflow_summary['runName']      = workflow.runName

        if (workflow.containerEngine) {

            workflow_summary['containerEngine'] = "$workflow.containerEngine"

            workflow_summary['containerEngine'] = workflow.containerEngine

        }

        if (workflow.container) {

            workflow_summary['container']       = "$workflow.container"

            workflow_summary['container'] = workflow.container

        }

        workflow_summary['launchDir']    = workflow.launchDir

        workflow_summary['workDir']      = workflow.workDir

                    def params_value = params.get(param)

                    def schema_value = group_params.get(param).default

                    def param_type   = group_params.get(param).type

                    if (schema_value == null) {

                        if (param_type == 'boolean') {

                            schema_value = false

                        }

                        if (param_type == 'string') {

                            schema_value = ''

                        }

                        if (param_type == 'integer') {

                            schema_value = 0

                        }

                    } else {

                    if (schema_value != null) {

                        if (param_type == 'string') {

                            if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {

                                def sub_string = schema_value.replace('\$projectDir', '')

                        }

                    }

                    if (params_value != schema_value) {

                        sub_params.put("$param", params_value)

                    // We have a default in the schema, and this isn't it

                    if (schema_value != null && params_value != schema_value) {

                        sub_params.put(param, params_value)

                    }

                    // No default in the schema, and this isn't empty

                    else if (schema_value == null && params_value != "" && params_value != null && params_value != false) {

                        sub_params.put(param, params_value)

                    }

                }

            }

     * Beautify parameters for summary and return as string

     */

    private static String params_summary_log(workflow, params, json_schema) {

        Map colors = log_colours(params.monochrome_logs)

        String output  = ''

        def params_map = params_summary_map(workflow, params, json_schema)

        def max_chars  = params_max_chars(params_map)

        for (group in params_map.keySet()) {

            def group_params = params_map.get(group)  // This gets the parameters of that particular group

            if (group_params) {

                output += group + '\n'

                output += colors.bold + group + colors.reset + '\n'

                for (param in group_params.keySet()) {

                    output += "    \u001B[1m" +  param.padRight(max_chars) + ": \u001B[1m" + group_params.get(param) + '\n'

                    output += "  " + colors.blue + param.padRight(max_chars) + ": " + colors.green +  group_params.get(param) + colors.reset + '\n'

                }

                output += '\n'

            }

        }

        output += "[Only displaying parameters that differ from pipeline default]\n"

        output += dashed_line(params.monochrome_logs)

        output += '\n\n' + dashed_line(params.monochrome_logs)

        output += colors.dim + "\n Only displaying parameters that differ from defaults.\n" + colors.reset

        output += dashed_line(params.monochrome_logs)

        return output

    }