mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
106 lines
3.6 KiB
Text
106 lines
3.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process CUSTOM_DUMPSOFTWAREVERSIONS {
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
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// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
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conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
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} else {
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container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
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}
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input:
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path versions
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output:
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path 'software_versions.yml' , emit: yml
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path 'software_versions_mqc.yml', emit: mqc_yml
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path 'versions.yml' , emit: versions
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script:
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"""
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#!/usr/bin/env python
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import yaml
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import platform
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from textwrap import dedent
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def _make_versions_html(versions):
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html = [
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dedent(
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'''\\
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<style>
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#nf-core-versions tbody:nth-child(even) {
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background-color: #f2f2f2;
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}
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</style>
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<table class="table" style="width:100%" id="nf-core-versions">
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<thead>
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<tr>
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<th> Process Name </th>
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<th> Software </th>
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<th> Version </th>
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</tr>
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</thead>
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'''
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)
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]
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for process, tmp_versions in sorted(versions.items()):
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html.append("<tbody>")
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for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
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html.append(
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dedent(
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f'''\\
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<tr>
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<td><samp>{process if (i == 0) else ''}</samp></td>
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<td><samp>{tool}</samp></td>
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<td><samp>{version}</samp></td>
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</tr>
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'''
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)
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)
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html.append("</tbody>")
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html.append("</table>")
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return "\\n".join(html)
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module_versions = {}
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module_versions["${getProcessName(task.process)}"] = {
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'python': platform.python_version(),
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'yaml': yaml.__version__
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}
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with open("$versions") as f:
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workflow_versions = yaml.safe_load(f) | module_versions
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workflow_versions["Workflow"] = {
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"Nextflow": "$workflow.nextflow.version",
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"$workflow.manifest.name": "$workflow.manifest.version"
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}
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versions_mqc = {
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'id': 'software_versions',
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'section_name': '${workflow.manifest.name} Software Versions',
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'section_href': 'https://github.com/${workflow.manifest.name}',
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'plot_type': 'html',
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'description': 'are collected at run time from the software output.',
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'data': _make_versions_html(workflow_versions)
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}
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with open("software_versions.yml", 'w') as f:
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yaml.dump(workflow_versions, f, default_flow_style=False)
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with open("software_versions_mqc.yml", 'w') as f:
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yaml.dump(versions_mqc, f, default_flow_style=False)
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with open('versions.yml', 'w') as f:
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yaml.dump(module_versions, f, default_flow_style=False)
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"""
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}
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