mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
* New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
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santiagorevale
GitHub
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commit
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12 changed files with 715 additions and 0 deletions
78
modules/gatk4/genotypegvcfs/functions.nf
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78
modules/gatk4/genotypegvcfs/functions.nf
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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)}/$args.filename"
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}
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}
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54
modules/gatk4/genotypegvcfs/main.nf
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54
modules/gatk4/genotypegvcfs/main.nf
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@ -0,0 +1,54 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GATK4_GENOTYPEGVCFS {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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}
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input:
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tuple val(meta), path(gvcf), path(gvcf_index)
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path fasta
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path fasta_index
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path fasta_dict
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path dbsnp
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path dbsnp_index
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path intervals_bed
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def dbsnp_options = dbsnp ? "-D ${dbsnp}" : ""
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def interval_options = intervals_bed ? "-L ${intervals_bed}" : ""
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def gvcf_options = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
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"""
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gatk \\
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GenotypeGVCFs \\
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$options.args \\
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$interval_options \\
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$dbsnp_options \\
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-R $fasta \\
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-V $gvcf_options \\
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-O ${prefix}.vcf.gz
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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69
modules/gatk4/genotypegvcfs/meta.yml
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69
modules/gatk4/genotypegvcfs/meta.yml
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name: gatk4_genotypegvcfs
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description: |
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Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
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keywords:
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- joint genotyping
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- genotype
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- gvcf
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tools:
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- gatk4:
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description: Genome Analysis Toolkit (GATK4)
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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tool_dev_url: https://github.com/broadinstitute/gatk
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doi: "10.1158/1538-7445.AM2017-3590"
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licence: ['BSD-3-clause']
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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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- gvcf:
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type: tuple of files
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description: |
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Tuple of gVCF(.gz) file (first) and its index (second) or the path to a GenomicsDB (and empty)
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pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"]
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- fasta:
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type: file
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description: Reference fasta file
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pattern: "*.fasta"
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- fasta_index:
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type: file
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description: Reference fasta index file
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pattern: "*.fai"
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- fasta_dict:
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type: file
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description: Reference fasta sequence dict file
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pattern: "*.dict"
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- dbsnp:
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type: file
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description: dbSNP VCF file
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pattern: "*.vcf.gz"
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- dbsnp_index:
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type: tuple of files
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description: dbSNP VCF index file
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pattern: "*.tbi"
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- intervals_bed:
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type: file
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description: An intevals BED file
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pattern: "*.bed"
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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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- vcf:
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type: file
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description: Genotyped VCF file
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pattern: "*.vcf.gz"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@santiagorevale"
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78
modules/gatk4/indexfeaturefile/functions.nf
Normal file
78
modules/gatk4/indexfeaturefile/functions.nf
Normal file
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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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|
//
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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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|
//
|
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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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|
|
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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
|
||||||
|
if (args.meta.containsKey(key)) {
|
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|
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
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|
}
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|
path = path instanceof String ? path : ''
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|
path_list.add(path)
|
||||||
|
}
|
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|
}
|
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|
}
|
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|
if (ioptions.publish_files instanceof Map) {
|
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|
for (ext in ioptions.publish_files) {
|
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|
if (args.filename.endsWith(ext.key)) {
|
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|
def ext_list = path_list.collect()
|
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|
ext_list.add(ext.value)
|
||||||
|
return "${getPathFromList(ext_list)}/$args.filename"
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else if (ioptions.publish_files == null) {
|
||||||
|
return "${getPathFromList(path_list)}/$args.filename"
|
||||||
|
}
|
||||||
|
}
|
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40
modules/gatk4/indexfeaturefile/main.nf
Normal file
40
modules/gatk4/indexfeaturefile/main.nf
Normal file
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|
@ -0,0 +1,40 @@
|
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|
// Import generic module functions
|
||||||
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
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|
|
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|
params.options = [:]
|
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|
options = initOptions(params.options)
|
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|
|
||||||
|
process GATK4_INDEXFEATUREFILE {
|
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|
tag "$meta.id"
|
||||||
|
label 'process_low'
|
||||||
|
publishDir "${params.outdir}",
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||||
|
|
||||||
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
|
||||||
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||||
|
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
|
||||||
|
} else {
|
||||||
|
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
|
||||||
|
}
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(feature_file)
|
||||||
|
|
||||||
|
output:
|
||||||
|
tuple val(meta), path("*.{tbi,idx}"), emit: index
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
script:
|
||||||
|
"""
|
||||||
|
gatk \\
|
||||||
|
IndexFeatureFile \\
|
||||||
|
$options.args \\
|
||||||
|
-I $feature_file
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
${getProcessName(task.process)}:
|
||||||
|
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
||||||
42
modules/gatk4/indexfeaturefile/meta.yml
Normal file
42
modules/gatk4/indexfeaturefile/meta.yml
Normal file
|
|
@ -0,0 +1,42 @@
|
||||||
|
name: gatk4_indexfeaturefile
|
||||||
|
description: Creates an index for a feature file, e.g. VCF or BED file.
|
||||||
|
keywords:
|
||||||
|
- index
|
||||||
|
- feature
|
||||||
|
tools:
|
||||||
|
- gatk4:
|
||||||
|
description: Genome Analysis Toolkit (GATK4)
|
||||||
|
homepage: https://gatk.broadinstitute.org/hc/en-us
|
||||||
|
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
|
||||||
|
tool_dev_url: https://github.com/broadinstitute/gatk
|
||||||
|
doi: "10.1158/1538-7445.AM2017-3590"
|
||||||
|
licence: ['BSD-3-clause']
|
||||||
|
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- feature_file:
|
||||||
|
type: file
|
||||||
|
description: VCF/BED file
|
||||||
|
pattern: "*.{vcf,vcf.gz,bed,bed.gz}"
|
||||||
|
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- index:
|
||||||
|
type: file
|
||||||
|
description: Index for VCF/BED file
|
||||||
|
pattern: "*.{tbi,idx}"
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@santiagorevale"
|
||||||
|
|
@ -474,6 +474,10 @@ gatk4/genomicsdbimport:
|
||||||
- modules/gatk4/genomicsdbimport/**
|
- modules/gatk4/genomicsdbimport/**
|
||||||
- tests/modules/gatk4/genomicsdbimport/**
|
- tests/modules/gatk4/genomicsdbimport/**
|
||||||
|
|
||||||
|
gatk4/genotypegvcfs:
|
||||||
|
- modules/gatk4/genotypegvcfs/**
|
||||||
|
- tests/modules/gatk4/genotypegvcfs/**
|
||||||
|
|
||||||
gatk4/getpileupsummaries:
|
gatk4/getpileupsummaries:
|
||||||
- modules/gatk4/getpileupsummaries/**
|
- modules/gatk4/getpileupsummaries/**
|
||||||
- tests/modules/gatk4/getpileupsummaries/**
|
- tests/modules/gatk4/getpileupsummaries/**
|
||||||
|
|
@ -482,6 +486,10 @@ gatk4/haplotypecaller:
|
||||||
- modules/gatk4/haplotypecaller/**
|
- modules/gatk4/haplotypecaller/**
|
||||||
- tests/modules/gatk4/haplotypecaller/**
|
- tests/modules/gatk4/haplotypecaller/**
|
||||||
|
|
||||||
|
gatk4/indexfeaturefile:
|
||||||
|
- modules/gatk4/indexfeaturefile/**
|
||||||
|
- tests/modules/gatk4/indexfeaturefile/**
|
||||||
|
|
||||||
gatk4/intervallisttools:
|
gatk4/intervallisttools:
|
||||||
- modules/gatk4/intervallisttools/**
|
- modules/gatk4/intervallisttools/**
|
||||||
- tests/modules/gatk4/intervallisttools/**
|
- tests/modules/gatk4/intervallisttools/**
|
||||||
|
|
|
||||||
|
|
@ -191,6 +191,8 @@ params {
|
||||||
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
||||||
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
||||||
|
|
||||||
|
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
||||||
|
|
||||||
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
|
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
|
||||||
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
||||||
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
|
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
|
||||||
|
|
|
||||||
180
tests/modules/gatk4/genotypegvcfs/main.nf
Normal file
180
tests/modules/gatk4/genotypegvcfs/main.nf
Normal file
|
|
@ -0,0 +1,180 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { GATK4_GENOTYPEGVCFS } from '../../../../modules/gatk4/genotypegvcfs/main.nf' addParams( options: [suffix:'.genotyped'] )
|
||||||
|
include { UNTAR } from '../../../../modules/untar/main.nf' addParams( options: [:] )
|
||||||
|
|
||||||
|
// Basic parameters with uncompressed VCF input
|
||||||
|
workflow test_gatk4_genotypegvcfs_vcf_input {
|
||||||
|
|
||||||
|
input = [ [ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true) ]
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters with compressed VCF input
|
||||||
|
workflow test_gatk4_genotypegvcfs_gz_input {
|
||||||
|
|
||||||
|
input = [ [ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters + optional dbSNP
|
||||||
|
workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
|
||||||
|
|
||||||
|
input = [ [ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||||
|
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, [] )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters + optional intervals
|
||||||
|
workflow test_gatk4_genotypegvcfs_gz_input_intervals {
|
||||||
|
|
||||||
|
input = [ [ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters + optional dbSNP + optional intervals
|
||||||
|
workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
|
||||||
|
|
||||||
|
input = [ [ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||||
|
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||||
|
|
||||||
|
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters with GenomicsDB input
|
||||||
|
workflow test_gatk4_genotypegvcfs_gendb_input {
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
|
||||||
|
|
||||||
|
UNTAR ( test_genomicsdb )
|
||||||
|
|
||||||
|
Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
|
||||||
|
Channel
|
||||||
|
.of([ id:'test' ])
|
||||||
|
.combine(UNTAR.out.untar)
|
||||||
|
.combine(mock_gvcf_index)
|
||||||
|
.set{ input }
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters with GenomicsDB + optional dbSNP
|
||||||
|
workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||||
|
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||||
|
|
||||||
|
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
|
||||||
|
|
||||||
|
UNTAR ( test_genomicsdb )
|
||||||
|
|
||||||
|
Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
|
||||||
|
Channel
|
||||||
|
.of([ id:'test' ])
|
||||||
|
.combine(UNTAR.out.untar)
|
||||||
|
.combine(mock_gvcf_index)
|
||||||
|
.set{ input }
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, [] )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters with GenomicsDB + optional intervals
|
||||||
|
workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||||
|
|
||||||
|
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
|
||||||
|
|
||||||
|
UNTAR ( test_genomicsdb )
|
||||||
|
|
||||||
|
Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
|
||||||
|
Channel
|
||||||
|
.of([ id:'test' ])
|
||||||
|
.combine(UNTAR.out.untar)
|
||||||
|
.combine(mock_gvcf_index)
|
||||||
|
.set{ input }
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
|
||||||
|
}
|
||||||
|
|
||||||
|
// Basic parameters with GenomicsDB + optional dbSNP + optional intervals
|
||||||
|
workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||||
|
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||||
|
|
||||||
|
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||||
|
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||||
|
|
||||||
|
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||||
|
|
||||||
|
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
|
||||||
|
|
||||||
|
UNTAR ( test_genomicsdb )
|
||||||
|
|
||||||
|
Channel.of(file("mock_gvcf_index.txt")).set{mock_gvcf_index}
|
||||||
|
Channel
|
||||||
|
.of([ id:'test' ])
|
||||||
|
.combine(UNTAR.out.untar)
|
||||||
|
.combine(mock_gvcf_index)
|
||||||
|
.set{ input }
|
||||||
|
|
||||||
|
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
|
||||||
|
}
|
||||||
80
tests/modules/gatk4/genotypegvcfs/test.yml
Normal file
80
tests/modules/gatk4/genotypegvcfs/test.yml
Normal file
|
|
@ -0,0 +1,80 @@
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_vcf_input
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_vcf_input -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
|
|
||||||
|
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
|
||||||
|
command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/genotypegvcfs
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genotyped.vcf.gz
|
||||||
|
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||||
45
tests/modules/gatk4/indexfeaturefile/main.nf
Normal file
45
tests/modules/gatk4/indexfeaturefile/main.nf
Normal file
|
|
@ -0,0 +1,45 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { GATK4_INDEXFEATUREFILE } from '../../../../modules/gatk4/indexfeaturefile/main.nf' addParams( options: [:] )
|
||||||
|
|
||||||
|
workflow test_gatk4_indexfeaturefile_bed {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
GATK4_INDEXFEATUREFILE ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_gatk4_indexfeaturefile_bed_gz {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
GATK4_INDEXFEATUREFILE ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_gatk4_indexfeaturefile_vcf {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
GATK4_INDEXFEATUREFILE ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_gatk4_indexfeaturefile_vcf_gz {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
GATK4_INDEXFEATUREFILE ( input )
|
||||||
|
}
|
||||||
39
tests/modules/gatk4/indexfeaturefile/test.yml
Normal file
39
tests/modules/gatk4/indexfeaturefile/test.yml
Normal file
|
|
@ -0,0 +1,39 @@
|
||||||
|
# We can't use an md5sum or check file contents because:
|
||||||
|
# a) the path to the file is embedded inside it,
|
||||||
|
# b) the file is binary so we can't check for text inside it.
|
||||||
|
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed
|
||||||
|
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/indexfeaturefile
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/genome.bed.idx
|
||||||
|
|
||||||
|
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed_gz
|
||||||
|
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/indexfeaturefile
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/genome.bed.gz.tbi
|
||||||
|
md5sum: 2eb6ed0a0b049efe4caa1413089dcd74
|
||||||
|
|
||||||
|
# We can't use an md5sum or check file contents because:
|
||||||
|
# a) the path to the file is embedded inside it,
|
||||||
|
# b) the file is binary so we can't check for text inside it.
|
||||||
|
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
|
||||||
|
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/indexfeaturefile
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genome.vcf.idx
|
||||||
|
|
||||||
|
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
|
||||||
|
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- gatk4
|
||||||
|
- gatk4/indexfeaturefile
|
||||||
|
files:
|
||||||
|
- path: output/gatk4/test.genome.vcf.gz.tbi
|
||||||
|
md5sum: ea03cd1d1f178eefa656787537053c37
|
||||||
Loading…
Reference in a new issue