mirror of
https://github.com/MillironX/nf-core_modules.git
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New module: LIMA (#719)
* 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 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 accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 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 accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 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 accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 🐛 FIX: Clean test_data.config * Update modules/lima/main.nf Add meta to each output Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/lima/main.nf Remove useless parenthesis Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 🐛 FIX: Keep version number only * 🐛 FIX: Reintegrate prefix variable and use it to define output file name * 👌 IMPROVE: add suffix arg to check output files names * 👌 IMPROVE: Use prefix for output filename * 🐛 FIX: Set optional output Allow usage of different input formats * 👌 IMPROVE: Update meta file * 👌 IMPROVE: Update test One test for each input file type * 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files * 👌 IMPROVE: Update with last templates / Follow new version.yaml rule * 🐛 FIX: Fix typos and include getProcessName function * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Using suffix to manage output was not a my best idea Add a bash code to detect extension and update output file name * 👌 IMPROVE: clean code Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
This commit is contained in:
Sébastien Guizard
GitHub
parent
906577873b
commit
4ec8b025bd
8 changed files with 390 additions and 0 deletions
2
.gitignore
vendored
2
.gitignore
vendored
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@ -11,3 +11,5 @@ __pycache__
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*.pyo
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*.pyc
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tests/data/
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modules/modtest/
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tests/modules/modtest/
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78
modules/lima/functions.nf
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78
modules/lima/functions.nf
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@ -0,0 +1,78 @@
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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)}/$args.filename"
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}
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}
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73
modules/lima/main.nf
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73
modules/lima/main.nf
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@ -0,0 +1,73 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process LIMA {
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tag "$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::lima=2.2.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0"
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} else {
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container "quay.io/biocontainers/lima:2.2.0--h9ee0642_0"
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}
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input:
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tuple val(meta), path(ccs)
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path primers
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output:
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tuple val(meta), path("*.clips") , emit: clips
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tuple val(meta), path("*.counts") , emit: counts
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tuple val(meta), path("*.guess") , emit: guess
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tuple val(meta), path("*.report") , emit: report
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tuple val(meta), path("*.summary"), emit: summary
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path "versions.yml" , emit: version
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tuple val(meta), path("*.bam") , optional: true, emit: bam
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tuple val(meta), path("*.bam.pbi") , optional: true, emit: pbi
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tuple val(meta), path("*.{fa, fasta}") , optional: true, emit: fasta
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tuple val(meta), path("*.{fa.gz, fasta.gz}"), optional: true, emit: fastagz
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tuple val(meta), path("*.fastq") , optional: true, emit: fastq
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tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
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tuple val(meta), path("*.xml") , optional: true, emit: xml
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tuple val(meta), path("*.json") , optional: true, emit: json
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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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OUT_EXT=""
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if [[ $ccs =~ bam\$ ]]; then
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OUT_EXT="bam"
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elif [[ $ccs =~ fasta\$ ]]; then
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OUT_EXT="fasta"
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elif [[ $ccs =~ fasta.gz\$ ]]; then
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OUT_EXT="fasta.gz"
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elif [[ $ccs =~ fastq\$ ]]; then
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OUT_EXT="fastq"
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elif [[ $ccs =~ fastq.gz\$ ]]; then
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OUT_EXT="fastq.gz"
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fi
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echo \$OUT_EXT
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lima \\
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$ccs \\
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$primers \\
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$prefix.\$OUT_EXT \\
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-j $task.cpus \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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lima: \$( lima --version | sed 's/lima //g' | sed 's/ (.\\+//g' )
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END_VERSIONS
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"""
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}
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77
modules/lima/meta.yml
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77
modules/lima/meta.yml
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@ -0,0 +1,77 @@
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name: lima
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description: lima - The PacBio Barcode Demultiplexer and Primer Remover
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keywords:
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- sort
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tools:
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- lima:
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description: lima - The PacBio Barcode Demultiplexer and Primer Remover
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homepage: https://github.com/PacificBiosciences/pbbioconda
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documentation: https://lima.how/
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tool_dev_url: https://github.com/pacificbiosciences/barcoding/
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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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- ccs:
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type: file
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description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs
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pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}"
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- primers:
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type: file
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description: Fasta file, sequences 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: A bam file of ccs purged of primers
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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 of ccs purged of primers
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pattern: "*.bam"
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- xml:
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type: file
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description: An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.
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pattern: "*.xml"
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- json:
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type: file
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description: A metadata json file
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pattern: "*.json"
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- clips:
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type: file
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description: A fasta file of clipped primers
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pattern: "*.clips"
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- counts:
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type: file
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description: A tabulated file of describing pairs of primers
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pattern: "*.counts"
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- guess:
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type: file
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description: A second tabulated file of describing pairs of primers (no doc available)
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pattern: "*.guess"
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- report:
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type: file
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description: A tab-separated file about each ZMW, unfiltered
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pattern: "*.report"
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- summary:
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type: file
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description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.
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pattern: "*.summary"
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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: "*.{version.txt}"
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authors:
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- "@sguizard"
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- modules/last/train/**
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- tests/modules/last/train/**
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lima:
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- modules/lima/**
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- tests/modules/lima/**
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lofreq/call:
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- modules/lofreq/call/**
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- tests/modules/lofreq/call/**
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@ -175,6 +175,11 @@ params {
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alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
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alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
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ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
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ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
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ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
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ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
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ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
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ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
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lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
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refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
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cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
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60
tests/modules/lima/main.nf
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60
tests/modules/lima/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { LIMA } from '../../../modules/lima/main.nf' addParams( options: [args: '--isoseq --peek-guess', suffix: ".fl"] )
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workflow test_lima_bam {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs'], 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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LIMA ( input, primers )
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}
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workflow test_lima_fa {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], 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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LIMA ( input, primers )
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}
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workflow test_lima_fa_gz {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], 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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LIMA ( input, primers )
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}
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workflow test_lima_fq {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], 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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LIMA ( input, primers )
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}
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workflow test_lima_fq_gz {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], 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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LIMA ( input, primers )
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}
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91
tests/modules/lima/test.yml
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91
tests/modules/lima/test.yml
Normal file
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- name: lima test_lima_bam
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command: nextflow run tests/modules/lima -entry test_lima_bam -c tests/config/nextflow.config
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tags:
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- lima
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files:
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- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam
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md5sum: 14b51d7f44e30c05a5b14e431a992097
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- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi
|
||||
md5sum: 6ae7f057304ad17dd9d5f565d72d3f7b
|
||||
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.consensusreadset.xml
|
||||
contains: [ 'ConsensusReadSet' ]
|
||||
- path: output/lima/test.fl.json
|
||||
contains: [ 'ConsensusReadSet' ]
|
||||
- path: output/lima/test.fl.lima.clips
|
||||
md5sum: fa03bc75bd78b2648a139fd67c69208f
|
||||
- path: output/lima/test.fl.lima.counts
|
||||
md5sum: 842c6a23ca2de504ced4538ad5111da1
|
||||
- path: output/lima/test.fl.lima.guess
|
||||
md5sum: d3675af3ca8a908ee9e3c231668392d3
|
||||
- path: output/lima/test.fl.lima.report
|
||||
md5sum: dc073985322ae0a003ccc7e0fa4db5e6
|
||||
- path: output/lima/test.fl.lima.summary
|
||||
md5sum: bcbcaaaca418bdeb91141c81715ca420
|
||||
|
||||
- name: lima test_lima_fa
|
||||
command: nextflow run tests/modules/lima -entry test_lima_fa -c tests/config/nextflow.config
|
||||
tags:
|
||||
- lima
|
||||
files:
|
||||
- path: output/lima/test.fl.lima.clips
|
||||
md5sum: 1012bc8874a14836f291bac48e8482a4
|
||||
- path: output/lima/test.fl.lima.counts
|
||||
md5sum: a4ceaa408be334eaa711577e95f8730e
|
||||
- path: output/lima/test.fl.lima.guess
|
||||
md5sum: 651e5f2b438b8ceadb3e06a2177e1818
|
||||
- path: output/lima/test.fl.lima.report
|
||||
md5sum: bd4a8bde17471563cf91aab4c787911d
|
||||
- path: output/lima/test.fl.lima.summary
|
||||
md5sum: 03be2311ba4afb878d8e547ab38c11eb
|
||||
|
||||
- name: lima test_lima_fa_gz
|
||||
command: nextflow run tests/modules/lima -entry test_lima_fa_gz -c tests/config/nextflow.config
|
||||
tags:
|
||||
- lima
|
||||
files:
|
||||
- path: output/lima/test.fl.lima.clips
|
||||
md5sum: 1012bc8874a14836f291bac48e8482a4
|
||||
- path: output/lima/test.fl.lima.counts
|
||||
md5sum: a4ceaa408be334eaa711577e95f8730e
|
||||
- path: output/lima/test.fl.lima.guess
|
||||
md5sum: 651e5f2b438b8ceadb3e06a2177e1818
|
||||
- path: output/lima/test.fl.lima.report
|
||||
md5sum: bd4a8bde17471563cf91aab4c787911d
|
||||
- path: output/lima/test.fl.lima.summary
|
||||
md5sum: 03be2311ba4afb878d8e547ab38c11eb
|
||||
|
||||
- name: lima test_lima_fq
|
||||
command: nextflow run tests/modules/lima -entry test_lima_fq -c tests/config/nextflow.config
|
||||
tags:
|
||||
- lima
|
||||
files:
|
||||
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq
|
||||
md5sum: ef395f689c5566f501e300bb83d7a5f2
|
||||
- path: output/lima/test.fl.lima.clips
|
||||
md5sum: 5c16ef8122f6f1798acc30eb8a30828c
|
||||
- path: output/lima/test.fl.lima.counts
|
||||
md5sum: 767b687e6eda7b24cd0e577f527eb2f0
|
||||
- path: output/lima/test.fl.lima.guess
|
||||
md5sum: 31b988aab6bda84867e704b9edd8a763
|
||||
- path: output/lima/test.fl.lima.report
|
||||
md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
|
||||
- path: output/lima/test.fl.lima.summary
|
||||
md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
|
||||
|
||||
- name: lima test_lima_fq_gz
|
||||
command: nextflow run tests/modules/lima -entry test_lima_fq_gz -c tests/config/nextflow.config
|
||||
tags:
|
||||
- lima
|
||||
files:
|
||||
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq.gz
|
||||
md5sum: 32c11db85f69a1b4454b6bbd794b6df2
|
||||
- path: output/lima/test.fl.lima.clips
|
||||
md5sum: 5c16ef8122f6f1798acc30eb8a30828c
|
||||
- path: output/lima/test.fl.lima.counts
|
||||
md5sum: 767b687e6eda7b24cd0e577f527eb2f0
|
||||
- path: output/lima/test.fl.lima.guess
|
||||
md5sum: 31b988aab6bda84867e704b9edd8a763
|
||||
- path: output/lima/test.fl.lima.report
|
||||
md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
|
||||
- path: output/lima/test.fl.lima.summary
|
||||
md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
|
||||
Loading…
Reference in a new issue