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Chromap Module (#659)
* Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remake chromap base files with new layout * Copy chromap * Copy index * Add compression * Update padding * Update container * Update chromap input test data * Add chromap chromap tests * Add padding * Update comment * update yaml file * Remove TODOs * Add fasta input to yaml * Update YAML * Remove comment, update container * Remove comments * Import Chromap index * Update test.yml * Fix read input * Update test.yml * Add bcftools/concat module. (#641) * draft for bcftools modules [ci skip] * initial test for bcftools concat * Update the params for testing * fix tests * Accomodate code review [ci skip] Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update the meta file and open PR for review * Update the keyword * Update the tags for module [ci skip[ * add threads Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add module for dragonflye (#633) * add module for dragonflye * fix tests for dragonflye * Update test.yml * Update meta.yml * Update main.nf * Update main.nf * Update modules/dragonflye/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update typos. change quote from ' to ". (#652) * Add bcftools/norm module (#655) * Initial draft [ci skip] * trigger first test * update output file path * Tests passing * finishing touches for meta.yml and update checksum * tweak checksum * add threads to the module * skip version info for matching test md5sum [ci skip] * Add ref fasta and finalize the module Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Expansionhunter (#666) Please enter the commit message for your changes. Lines starting * adds expansionhunter module Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update test.yml (#668) * Specify in guidelines one should split CPUs when module has n > 1 tool (#660) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Describe CPU splitting * Update README.md Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * More CPU examples Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Add dsh-bio export-segments module (#631) Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update: `BWA/ALN` (#653) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate. Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Update seqwish reported version to match bioconda version. (#678) * Bbmap index (#683) BBMap index module * Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remove unnecessary files * Remove unnecessary files * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove pytest_software.yml * Apply suggestions from code review Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com> Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Mahesh Binzer-Panchal
GitHub
parent
561f16fe74
commit
58134cb929
11 changed files with 529 additions and 0 deletions
68
modules/chromap/chromap/functions.nf
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68
modules/chromap/chromap/functions.nf
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@ -0,0 +1,68 @@
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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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// 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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if (!args.filename.endsWith('.version.txt')) {
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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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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)}/$args.filename"
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}
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}
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}
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93
modules/chromap/chromap/main.nf
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93
modules/chromap/chromap/main.nf
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@ -0,0 +1,93 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = 0.1 // No version information printed
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process CHROMAP_CHROMAP {
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tag "$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::chromap=0.1 bioconda::samtools=1.13" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0"
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}
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input:
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tuple val(meta), path(reads)
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path fasta
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path index
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path barcodes
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path whitelist
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path chr_order
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path pairs_chr_order
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output:
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tuple val(meta), path("*.bed.gz") , optional:true, emit: bed
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tuple val(meta), path("*.bam") , optional:true, emit: bam
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tuple val(meta), path("*.tagAlign.gz"), optional:true, emit: tagAlign
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tuple val(meta), path("*.pairs.gz") , optional:true, emit: pairs
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def args = options.args.tokenize()
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def file_extension = options.args.contains("--SAM")? 'sam' :
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options.args.contains("--TagAlign")? 'tagAlign' :
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options.args.contains("--pairs")? 'pairs' : 'bed'
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if (barcodes) {
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args << "-b ${barcodes.join(',')}"
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if (whitelist) {
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args << "--barcode-whitelist $whitelist"
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}
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}
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if (chr_order) {
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args << "--chr-order $chr_order"
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}
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if (pairs_chr_order){
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args << "--pairs-natural-chr-order $pairs_chr_order"
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}
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def compression_cmds = """
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gzip ${prefix}.${file_extension}
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"""
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if (options.args.contains("--SAM")) {
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compression_cmds = """
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samtools view $options.args2 -@ ${task.cpus} -bh \\
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-o ${prefix}.bam ${prefix}.${file_extension}
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rm ${prefix}.${file_extension}
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samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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if (meta.single_end) {
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"""
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chromap ${args.join(' ')} \\
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-t $task.cpus \\
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-x $index \\
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-r $fasta \\
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-1 ${reads.join(',')} \\
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-o ${prefix}.${file_extension}
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echo "$VERSION" > ${software}.version.txt
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""" + compression_cmds
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} else {
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"""
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chromap ${args.join(' ')} \\
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-t $task.cpus \\
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-x $index \\
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-r $fasta \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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-o ${prefix}.${file_extension}
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echo "$VERSION" > ${software}.version.txt
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""" + compression_cmds
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}
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}
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88
modules/chromap/chromap/meta.yml
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88
modules/chromap/chromap/meta.yml
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@ -0,0 +1,88 @@
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name: chromap_chromap
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description: |
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Performs preprocessing and alignment of chromatin fastq files to
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fasta reference files using chromap.
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keywords:
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- chromap
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- alignment
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- map
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- fastq
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- bam
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- sam
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- hi-c
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- atac-seq
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- chip-seq
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- trimming
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- duplicate removal
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tools:
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- chromap:
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description: Fast alignment and preprocessing of chromatin profiles
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homepage: https://github.com/haowenz/chromap
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documentation: https://github.com/haowenz/chromap
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tool_dev_url: https://github.com/haowenz/chromap
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doi: ""
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licence: ['GPL v3']
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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', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- fasta:
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type: file
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description: |
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The fasta reference file.
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- index:
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type: file
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description: |
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Chromap genome index files (*.index)
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- barcodes:
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type: file
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description: |
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Cell barcode files
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- whitelist:
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type: file
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description: |
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Cell barcode whitelist file
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- chr_order:
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type: file
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description: |
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Custom chromosome order
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- pairs_chr_order:
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type: file
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description: |
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Natural chromosome order for pairs flipping
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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: "*.{version.txt}"
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- bed:
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type: file
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description: BED file
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pattern: "*.bed.gz"
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- bam:
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type: file
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description: BAM file
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pattern: "*.bam"
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- tagAlign:
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type: file
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description: tagAlign file
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pattern: "*.tagAlign.gz"
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- pairs:
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type: file
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description: pairs file
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pattern: "*.pairs.gz"
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authors:
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- "@mahesh-panchal"
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68
modules/chromap/index/functions.nf
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68
modules/chromap/index/functions.nf
Normal file
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@ -0,0 +1,68 @@
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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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// 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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if (!args.filename.endsWith('.version.txt')) {
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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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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)}/$args.filename"
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}
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}
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}
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40
modules/chromap/index/main.nf
Normal file
40
modules/chromap/index/main.nf
Normal file
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@ -0,0 +1,40 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = 0.1 // No version information printed
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process CHROMAP_INDEX {
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tag '$fasta'
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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:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0"
|
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}
|
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|
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input:
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path fasta
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output:
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path "*.index" , emit: index
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = fasta.baseName
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"""
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chromap -i $options.args \\
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-t $task.cpus \\
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-r $fasta \\
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-o ${prefix}.index
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echo "$VERSION" > ${software}.version.txt
|
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"""
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}
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33
modules/chromap/index/meta.yml
Normal file
33
modules/chromap/index/meta.yml
Normal file
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@ -0,0 +1,33 @@
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name: chromap_index
|
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description: Indexes a fasta reference genome ready for chromatin profiling.
|
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keywords:
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- index
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- fasta
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- genome
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- reference
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tools:
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- chromap:
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description: Fast alignment and preprocessing of chromatin profiles
|
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homepage: https://github.com/haowenz/chromap
|
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documentation: https://github.com/haowenz/chromap
|
||||
tool_dev_url: https://github.com/haowenz/chromap
|
||||
doi: ""
|
||||
licence: ['GPL v3']
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Fasta reference file.
|
||||
|
||||
output:
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.{version.txt}"
|
||||
- index:
|
||||
type: file
|
||||
description: Index file of the reference genome
|
||||
pattern: "*.{index}"
|
||||
|
||||
authors:
|
||||
- "@mahesh-panchal"
|
||||
|
|
@ -226,6 +226,14 @@ cat/fastq:
|
|||
- modules/cat/fastq/**
|
||||
- tests/modules/cat/fastq/**
|
||||
|
||||
chromap/chromap:
|
||||
- modules/chromap/chromap/**
|
||||
- tests/modules/chromap/chromap/**
|
||||
|
||||
chromap/index:
|
||||
- modules/chromap/index/**
|
||||
- tests/modules/chromap/index/**
|
||||
|
||||
cnvkit:
|
||||
- modules/cnvkit/**
|
||||
- tests/modules/cnvkit/**
|
||||
|
|
|
|||
79
tests/modules/chromap/chromap/main.nf
Normal file
79
tests/modules/chromap/chromap/main.nf
Normal file
|
|
@ -0,0 +1,79 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf' addParams( options: [:] )
|
||||
include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../modules/chromap/chromap/main.nf' addParams( options: [:] )
|
||||
include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM } from '../../../../modules/chromap/chromap/main.nf' addParams( options: ['args': '--SAM'] )
|
||||
|
||||
workflow test_chromap_chromap_single_end {
|
||||
|
||||
// Test single-end and gz compressed output
|
||||
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
input = [
|
||||
[ id:'test', single_end:true ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
CHROMAP_INDEX ( fasta )
|
||||
CHROMAP_CHROMAP_BASE (
|
||||
input, // meta + read data
|
||||
fasta, // reference genome
|
||||
CHROMAP_INDEX.out.index, // reference index
|
||||
[], // barcode file
|
||||
[], // barcode whitelist
|
||||
[], // chromosome order file
|
||||
[] // pairs chromosome order file
|
||||
)
|
||||
}
|
||||
|
||||
workflow test_chromap_chromap_paired_end {
|
||||
|
||||
// Test paired-end and gz compressed output
|
||||
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
[
|
||||
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
]
|
||||
|
||||
CHROMAP_INDEX ( fasta )
|
||||
CHROMAP_CHROMAP_BASE (
|
||||
input, // meta + read data
|
||||
fasta, // reference genome
|
||||
CHROMAP_INDEX.out.index, // reference index
|
||||
[], // barcode file
|
||||
[], // barcode whitelist
|
||||
[], // chromosome order file
|
||||
[] // pairs chromosome order file
|
||||
)
|
||||
}
|
||||
|
||||
workflow test_chromap_chromap_paired_bam {
|
||||
|
||||
// Test paired-end and bam output
|
||||
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
[
|
||||
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
]
|
||||
|
||||
CHROMAP_INDEX ( fasta )
|
||||
CHROMAP_CHROMAP_SAM (
|
||||
input, // meta + read data
|
||||
fasta, // reference genome
|
||||
CHROMAP_INDEX.out.index, // reference index
|
||||
[], // barcode file
|
||||
[], // barcode whitelist
|
||||
[], // chromosome order file
|
||||
[] // pairs chromosome order file
|
||||
)
|
||||
}
|
||||
32
tests/modules/chromap/chromap/test.yml
Normal file
32
tests/modules/chromap/chromap/test.yml
Normal file
|
|
@ -0,0 +1,32 @@
|
|||
- name: chromap chromap test_chromap_chromap_single_end
|
||||
command: nextflow run tests/modules/chromap/chromap -entry test_chromap_chromap_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- chromap/chromap
|
||||
- chromap
|
||||
files:
|
||||
- path: output/chromap/genome.index
|
||||
md5sum: f889d5f61d80823766af33277d27d386
|
||||
- path: output/chromap/test.bed.gz
|
||||
md5sum: 7029066c27ac6f5ef18d660d5741979a
|
||||
|
||||
- name: chromap chromap test_chromap_chromap_paired_end
|
||||
command: nextflow run tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- chromap/chromap
|
||||
- chromap
|
||||
files:
|
||||
- path: output/chromap/genome.index
|
||||
md5sum: f889d5f61d80823766af33277d27d386
|
||||
- path: output/chromap/test.bed.gz
|
||||
md5sum: cafd8fb21977f5ae69e9008b220ab169
|
||||
|
||||
- name: chromap chromap test_chromap_chromap_paired_bam
|
||||
command: nextflow run tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c tests/config/nextflow.config
|
||||
tags:
|
||||
- chromap/chromap
|
||||
- chromap
|
||||
files:
|
||||
- path: output/chromap/genome.index
|
||||
md5sum: f889d5f61d80823766af33277d27d386
|
||||
- path: output/chromap/test.bam
|
||||
md5sum: bd1e3fe0f3abd1430ae191754f16a3ed
|
||||
12
tests/modules/chromap/index/main.nf
Normal file
12
tests/modules/chromap/index/main.nf
Normal file
|
|
@ -0,0 +1,12 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_chromap_index {
|
||||
|
||||
input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
CHROMAP_INDEX ( input )
|
||||
}
|
||||
8
tests/modules/chromap/index/test.yml
Normal file
8
tests/modules/chromap/index/test.yml
Normal file
|
|
@ -0,0 +1,8 @@
|
|||
- name: chromap index test_chromap_index
|
||||
command: nextflow run tests/modules/chromap/index -entry test_chromap_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- chromap/index
|
||||
- chromap
|
||||
files:
|
||||
- path: output/chromap/genome.index
|
||||
md5sum: f889d5f61d80823766af33277d27d386
|
||||
Loading…
Reference in a new issue