nf-core_modules/modules/custom/dumpsoftwareversions/main.nf

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process CUSTOM_DUMPSOFTWAREVERSIONS {
    label 'process_low'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }

    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
    } else {
        container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
    }

    input:
    path versions

    output:
    path "software_versions.yml"    , emit: yml
    path "software_versions_mqc.yml", emit: mqc_yml
    path "versions.yml"             , emit: versions

    script:
    """
    #!/usr/bin/env python

    import yaml
    import platform
    from textwrap import dedent

    def _make_versions_html(versions):
        html = [
            dedent(
                '''\\
                <style>
                #nf-core-versions tbody:nth-child(even) {
                    background-color: #f2f2f2;
                }
                </style>
                <table class="table" style="width:100%" id="nf-core-versions">
                    <thead>
                        <tr>
                            <th> Process Name </th>
                            <th> Software </th>
                            <th> Version  </th>
                        </tr>
                    </thead>
                '''
            )
        ]
        for process, tmp_versions in sorted(versions.items()):
            html.append("<tbody>")
            for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
                html.append(
                    dedent(
                        f'''\\
                        <tr>
                            <td><samp>{process if (i == 0) else ''}</samp></td>
                            <td><samp>{tool}</samp></td>
                            <td><samp>{version}</samp></td>
                        </tr>
                        '''
                    )
                )
            html.append("</tbody>")
        html.append("</table>")
        return "\\n".join(html)

    module_versions = {}
    module_versions["${getProcessName(task.process)}"] = {
        'python': platform.python_version(),
        'yaml': yaml.__version__
    }

    with open("$versions") as f:
        workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions

    workflow_versions["Workflow"] = {
        "Nextflow": "$workflow.nextflow.version",
        "$workflow.manifest.name": "$workflow.manifest.version"
    }

    versions_mqc = {
        'id': 'software_versions',
        'section_name': '${workflow.manifest.name} Software Versions',
        'section_href': 'https://github.com/${workflow.manifest.name}',
        'plot_type': 'html',
        'description': 'are collected at run time from the software output.',
        'data': _make_versions_html(workflow_versions)
    }

    with open("software_versions.yml", 'w') as f:
        yaml.dump(workflow_versions, f, default_flow_style=False)
    with open("software_versions_mqc.yml", 'w') as f:
        yaml.dump(versions_mqc, f, default_flow_style=False)

    with open('versions.yml', 'w') as f:
        yaml.dump(module_versions, f, default_flow_style=False)
    """
}