New module: `isoseq3/refine` (#748)
* 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 🐛 FIX: Remove unwanted files * 🐛 FIX: Protect \ * 🐛 FIX: Remove test files * Apply suggestions from code review * Apply suggestions from code review * Update tests/modules/isoseq3/refine/test.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>unifiedgenotyper
Sébastien Guizard
3 years ago
committed by
GitHub
parent
84f2302920
commit
79d38a306b
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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)}/$args.filename"
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}
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}
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process ISOSEQ3_REFINE {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0"
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} else {
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container "quay.io/biocontainers/isoseq3:3.4.0--0"
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}
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input:
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tuple val(meta), path(bam)
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path primers
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.bam.pbi") , emit: pbi
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tuple val(meta), path("*.consensusreadset.xml"), emit: consensusreadset
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tuple val(meta), path("*.filter_summary.json") , emit: summary
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tuple val(meta), path("*.report.csv") , emit: report
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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isoseq3 \\
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refine \\
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-j $task.cpus \\
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$options.args \\
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$bam \\
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$primers \\
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${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( isoseq3 refine --version|sed 's/isoseq refine //'|sed 's/ (commit.\\+//' )
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END_VERSIONS
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"""
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}
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name: isoseq3_refine
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description: Generate transcripts by clustering HiFi reads
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keywords:
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- isoseq3
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- isoseq3/refine
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tools:
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- isoseq3:
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description: IsoSeq3 - Scalable De Novo Isoform Discovery
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homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
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documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
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tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
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doi: ""
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licence: ['BSD-3-clause-Clear']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test ]
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- bam:
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type: file
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description: BAM file, cleaned ccs generated by lima
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pattern: "*.bam"
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- primers:
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type: file
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description: fasta file of primers
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pattern: "*.fasta"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- bam:
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type: file
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description: Set of complete reads (with polyA tail), where the polyA has been trimmed
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pattern: "*.bam"
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- pbi:
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type: file
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description: Pacbio index file from polyA trimmed reads
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pattern: "*.pbi"
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- consensusreadset:
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type: file
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description: Metadata about read library
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pattern: "*.xml"
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- summary:
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type: file
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description: json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads
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pattern: "*.json"
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- report:
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type: file
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description: Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)
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pattern: "*.csv"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@sguizard"
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ISOSEQ3_REFINE } from '../../../../modules/isoseq3/refine/main' addParams( options: [suffix:'.refine'] )
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workflow test_isoseq3_refine {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['lima'], checkIfExists: true),
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]
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primers = file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true)
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ISOSEQ3_REFINE ( input, primers )
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}
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@ -0,0 +1,16 @@
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- name: isoseq3 refine test_isoseq3_refine
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command: nextflow run tests/modules/isoseq3/refine -entry test_isoseq3_refine -c tests/config/nextflow.config
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tags:
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- isoseq3
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- isoseq3/refine
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files:
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- path: output/isoseq3/test.refine.bam
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md5sum: e8387afd5f66a7f6a89f90a0dcf3b823
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- path: output/isoseq3/test.refine.bam.pbi
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md5sum: 8097cad9e472f2f79de6de5fe3dcc822
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- path: output/isoseq3/test.refine.consensusreadset.xml
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contains: [ 'pbds:ConsensusReadSet' ]
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- path: output/isoseq3/test.refine.filter_summary.json
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md5sum: 87f8bdd5c60741f47b8a991e002f7ef3
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- path: output/isoseq3/test.refine.report.csv
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md5sum: d42a139e5d9b08396bdb087c01243ea9
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