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Add custom/dumpsoftwareversions modules for nf-core pipeline template (#761)
* Add custom/dumpsoftwareversions modules for nf-core pipeline template * Remove md5sums due to differing NF versions
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6 changed files with 256 additions and 4 deletions
78
modules/custom/dumpsoftwareversions/functions.nf
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78
modules/custom/dumpsoftwareversions/functions.nf
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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105
modules/custom/dumpsoftwareversions/main.nf
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105
modules/custom/dumpsoftwareversions/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process CUSTOM_DUMPSOFTWAREVERSIONS {
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label 'process_low'
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publishDir "${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_yaml
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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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with open("$versions") as f:
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versions = yaml.safe_load(f)
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versions["Workflow"] = {
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"Nextflow": "$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(versions)
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}
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with open("software_versions.yml", 'w') as f:
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yaml.dump(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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yaml_version = {}
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yaml_version["${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.yml', 'w') as f:
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yaml.dump(yaml_version, f, default_flow_style=False)
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"""
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}
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33
modules/custom/dumpsoftwareversions/meta.yml
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33
modules/custom/dumpsoftwareversions/meta.yml
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name: custom_dumpsoftwareversions
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description: Custom module used to dump software versions within the nf-core pipeline template
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keywords:
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- custom
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- version
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tools:
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- custom:
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description: Custom module used to dump software versions within the nf-core pipeline template
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homepage: https://github.com/nf-core/tools
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documentation: https://github.com/nf-core/tools
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input:
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- versions:
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type: file
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description: YML file containing software versions
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pattern: "*.yml"
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output:
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- yml:
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type: file
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description: Standard YML file containing software versions
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pattern: "software_versions.yml"
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- mqc_yml:
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type: file
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description: MultiQC custom content YML file containing software versions
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pattern: "software_versions_mqc.yml"
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- version:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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authors:
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- "@drpatelh"
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@ -258,6 +258,10 @@ cooler/dump:
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- modules/cooler/dump/**
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- tests/modules/cooler/dump/**
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custom/dumpsoftwareversions:
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- modules/custom/dumpsoftwareversions/**
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- tests/modules/custom/dumpsoftwareversions/**
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cutadapt:
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- modules/cutadapt/**
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- tests/modules/cutadapt/**
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- modules/delly/call/**
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- tests/modules/delly/call/**
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diamond/blastx:
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- modules/diamond/blastx/**
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- tests/modules/diamond/blastx/**
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diamond/blastp:
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- modules/diamond/blastp/**
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- tests/modules/diamond/blastp/**
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diamond/blastx:
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- modules/diamond/blastx/**
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- tests/modules/diamond/blastx/**
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diamond/makedb:
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- modules/diamond/makedb/**
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- tests/modules/diamond/makedb/**
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24
tests/modules/custom/dumpsoftwareversions/main.nf
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24
tests/modules/custom/dumpsoftwareversions/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FASTQC } from '../../../../modules/fastqc/main.nf' addParams( options: [:] )
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include { MULTIQC } from '../../../../modules/multiqc/main.nf' addParams( options: [:] )
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include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf' addParams( options: [publish_dir:'custom'] )
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workflow test_custom_dumpsoftwareversions {
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input = [
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[ id: 'test', single_end: false ],
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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FASTQC ( input )
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MULTIQC ( FASTQC.out.zip.collect { it[1] } )
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ch_software_versions = Channel.empty()
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ch_software_versions = ch_software_versions.mix(FASTQC.out.version)
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ch_software_versions = ch_software_versions.mix(MULTIQC.out.version)
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CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
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}
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8
tests/modules/custom/dumpsoftwareversions/test.yml
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8
tests/modules/custom/dumpsoftwareversions/test.yml
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- name: custom dumpsoftwareversions
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command: nextflow run ./tests/modules/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c tests/config/nextflow.config
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tags:
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- custom
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- custom/dumpsoftwareversions
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files:
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- path: output/custom/software_versions.yml
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- path: output/custom/software_versions_mqc.yml
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