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
This commit is contained in:
Harshil Patel 2021-09-29 14:27:00 +01:00 committed by GitHub
parent b932210f27
commit b2c2d4deb4
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
6 changed files with 256 additions and 4 deletions

View file

@ -0,0 +1,78 @@
//
// Utility functions used in nf-core DSL2 module files
//
//
// Extract name of software tool from process name using $task.process
//
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
}
path = path instanceof String ? path : ''
path_list.add(path)
}
}
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}

View file

@ -0,0 +1,105 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process CUSTOM_DUMPSOFTWAREVERSIONS {
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
}
input:
path versions
output:
path 'software_versions.yml' , emit: yml
path 'software_versions_mqc.yml', emit: mqc_yaml
path 'versions.yml' , emit: versions
script:
"""
#!/usr/bin/env python
import yaml
import platform
from textwrap import dedent
def _make_versions_html(versions):
html = [
dedent(
'''\\
<style>
#nf-core-versions tbody:nth-child(even) {
background-color: #f2f2f2;
}
</style>
<table class="table" style="width:100%" id="nf-core-versions">
<thead>
<tr>
<th> Process Name </th>
<th> Software </th>
<th> Version </th>
</tr>
</thead>
'''
)
]
for process, tmp_versions in sorted(versions.items()):
html.append("<tbody>")
for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
html.append(
dedent(
f'''\\
<tr>
<td><samp>{process if (i == 0) else ''}</samp></td>
<td><samp>{tool}</samp></td>
<td><samp>{version}</samp></td>
</tr>
'''
)
)
html.append("</tbody>")
html.append("</table>")
return "\\n".join(html)
with open("$versions") as f:
versions = yaml.safe_load(f)
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/${workflow.manifest.name}',
'plot_type': 'html',
'description': 'are collected at run time from the software output.',
'data': _make_versions_html(versions)
}
with open("software_versions.yml", 'w') as f:
yaml.dump(versions, f, default_flow_style=False)
with open("software_versions_mqc.yml", 'w') as f:
yaml.dump(versions_mqc, f, default_flow_style=False)
yaml_version = {}
yaml_version["${getProcessName(task.process)}"] = {
'python': platform.python_version(),
'yaml': yaml.__version__
}
with open('versions.yml', 'w') as f:
yaml.dump(yaml_version, f, default_flow_style=False)
"""
}

View file

@ -0,0 +1,33 @@
name: custom_dumpsoftwareversions
description: Custom module used to dump software versions within the nf-core pipeline template
keywords:
- custom
- version
tools:
- custom:
description: Custom module used to dump software versions within the nf-core pipeline template
homepage: https://github.com/nf-core/tools
documentation: https://github.com/nf-core/tools
input:
- versions:
type: file
description: YML file containing software versions
pattern: "*.yml"
output:
- yml:
type: file
description: Standard YML file containing software versions
pattern: "software_versions.yml"
- mqc_yml:
type: file
description: MultiQC custom content YML file containing software versions
pattern: "software_versions_mqc.yml"
- version:
type: file
description: File containing software version
pattern: "versions.yml"
authors:
- "@drpatelh"

View file

@ -258,6 +258,10 @@ cooler/dump:
- modules/cooler/dump/**
- tests/modules/cooler/dump/**
custom/dumpsoftwareversions:
- modules/custom/dumpsoftwareversions/**
- tests/modules/custom/dumpsoftwareversions/**
cutadapt:
- modules/cutadapt/**
- tests/modules/cutadapt/**
@ -286,14 +290,14 @@ delly/call:
- modules/delly/call/**
- tests/modules/delly/call/**
diamond/blastx:
- modules/diamond/blastx/**
- tests/modules/diamond/blastx/**
diamond/blastp:
- modules/diamond/blastp/**
- tests/modules/diamond/blastp/**
diamond/blastx:
- modules/diamond/blastx/**
- tests/modules/diamond/blastx/**
diamond/makedb:
- modules/diamond/makedb/**
- tests/modules/diamond/makedb/**

View file

@ -0,0 +1,24 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FASTQC } from '../../../../modules/fastqc/main.nf' addParams( options: [:] )
include { MULTIQC } from '../../../../modules/multiqc/main.nf' addParams( options: [:] )
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf' addParams( options: [publish_dir:'custom'] )
workflow test_custom_dumpsoftwareversions {
input = [
[ id: 'test', single_end: false ],
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
FASTQC ( input )
MULTIQC ( FASTQC.out.zip.collect { it[1] } )
ch_software_versions = Channel.empty()
ch_software_versions = ch_software_versions.mix(FASTQC.out.version)
ch_software_versions = ch_software_versions.mix(MULTIQC.out.version)
CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
}

View file

@ -0,0 +1,8 @@
- name: custom dumpsoftwareversions
command: nextflow run ./tests/modules/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c tests/config/nextflow.config
tags:
- custom
- custom/dumpsoftwareversions
files:
- path: output/custom/software_versions.yml
- path: output/custom/software_versions_mqc.yml