New module: `isoseq3/cluster` (#801)
* 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 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) * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 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: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 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 * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update code to new versions capture + better output channels * 👌 IMPROVE: Update with new versions.yml file * 🐛 FIX: Update meta.yml + correct typos * 👌 IMPROVE: Clean output file names + correct typo * 🐛 FIX: Remove bamtools/split module from isoseq3/clusterunifiedgenotyper
Sébastien Guizard
3 years ago
committed by
GitHub
parent
79d38a306b
commit
5a49d2c1bf
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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)}/$args.filename"
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}
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}
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process ISOSEQ3_CLUSTER {
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tag "$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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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("*.cluster") , emit: cluster
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tuple val(meta), path("*.cluster_report.csv"), emit: cluster_report
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tuple val(meta), path("*.transcriptset.xml") , emit: transcriptset
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tuple val(meta), path("*.hq.bam") , emit: hq_bam
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tuple val(meta), path("*.hq.bam.pbi") , emit: hq_pbi
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tuple val(meta), path("*.lq.bam") , emit: lq_bam
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tuple val(meta), path("*.lq.bam.pbi") , emit: lq_pbi
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.singletons.bam") , optional: true, emit: singletons_bam
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tuple val(meta), path("*.singletons.bam.pbi"), optional: true, emit: singletons_pbi
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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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cluster \\
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$bam \\
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${prefix}.bam \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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isoseq3 cluster: \$( isoseq3 cluster --version|sed 's/isoseq cluster //g'|sed 's/ (.*//g' )
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END_VERSIONS
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"""
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}
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@ -0,0 +1,81 @@
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name: isoseq3_cluster
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description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
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keywords:
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- cluster
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tools:
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- isoseq3:
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description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
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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 generated by isoseq3 refine
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pattern: "*.bam"
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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', single_end:false ]
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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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- bam:
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type: file
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description: BAM file of clustered consensus
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pattern: "*.bam"
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- pbi:
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type: file
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description: Pacbio Index of consensus reads generated by clustering
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pattern: "*.pbi"
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- cluster:
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type: file
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description: A two columns (from, to) file describing original read name to new read name
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pattern: "*.cluster"
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- cluster_report:
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type: file
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description: A table files clusters (transcripts) members (read)
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pattern: "*.cluster_report.csv"
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- transcriptset:
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type: file
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description: A metadata xml file which contains full paths to data files
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pattern: "*.clustered.transcriptset.xml"
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- hq_bam:
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type: file
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description: High quality reads
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pattern: "*.hq.bam"
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- hq_pbi:
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type: file
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description: Pacbio index of high quality reads
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pattern: "*.hq.bam.pbi"
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- lq_bam:
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type: file
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description: Low quality reads
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pattern: "*.lq.bam"
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- lq_pbi:
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type: file
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description: Pacbio index of low quality reads
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pattern: "*.lq.bam.pbi"
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- singletons_bam:
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type: file
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description: Unclustered reads
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pattern: "*.singletons.bam"
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- singletons_pbi:
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type: file
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description: Pacbio index of unclustered reads
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pattern: "*.singletons.bam.pbi"
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authors:
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- "@sguizard"
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@ -0,0 +1,15 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ISOSEQ3_CLUSTER } from '../../../../modules/isoseq3/cluster/main.nf' addParams( options: [args: '--singletons --use-qvs --verbose'] )
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workflow test_isoseq3_cluster {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['refine'], checkIfExists: true),
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]
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ISOSEQ3_CLUSTER ( input )
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}
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@ -0,0 +1,28 @@
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- name: isoseq3 cluster test_isoseq3_cluster
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command: nextflow run tests/modules/isoseq3/cluster -entry test_isoseq3_cluster -c tests/config/nextflow.config
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tags:
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- isoseq3
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- isoseq3/cluster
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files:
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- path: output/isoseq3/test.bam
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md5sum: ca8277f4d8fe1bba68ba266c42b46dd1
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- path: output/isoseq3/test.bam.pbi
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md5sum: cbc06657b4543faba7ff886b3b12b862
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- path: output/isoseq3/test.cluster
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md5sum: d5059d856763fc5591332980bfc0d57b
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- path: output/isoseq3/test.cluster_report.csv
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md5sum: 342d97dc10aedf80a45977edcb491c62
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- path: output/isoseq3/test.hq.bam
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md5sum: e93ea85776c35c246364d954032c2ea9
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- path: output/isoseq3/test.hq.bam.pbi
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md5sum: 5a8ea7668e8f8e173478b28cbb6ab515
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- path: output/isoseq3/test.lq.bam
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md5sum: 4ea0e4f4a6cc689dcc275adcdf688fad
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- path: output/isoseq3/test.lq.bam.pbi
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md5sum: f5edc24711b2c8d6474d60cb69022af0
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- path: output/isoseq3/test.singletons.bam
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md5sum: 73d131920bd42e1fc5fca2e6cb71f4b2
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- path: output/isoseq3/test.singletons.bam.pbi
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md5sum: 73980863be4b5bda2846325c737f0b5e
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- path: output/isoseq3/test.transcriptset.xml
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contains: [ 'PacBio.DataSet.TranscriptSet' ]
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