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new module: gubbins (#377)
* new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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60
software/gubbins/functions.nf
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60
software/gubbins/functions.nf
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/*
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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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* 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_id = args.publish_by_id ?: false
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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_id) {
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path_list.add(args.publish_id)
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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)}/$args.filename"
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}
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}
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}
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44
software/gubbins/main.nf
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44
software/gubbins/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GUBBINS {
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label 'process_medium'
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publishDir "${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), publish_id:'') }
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conda (params.enable_conda ? "bioconda::gubbins=2.4.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gubbins:2.4.1--py38h197edbe_1"
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} else {
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container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
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}
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input:
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path alignment
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output:
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path "*.fasta" , emit: fasta
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path "*.gff" , emit: gff
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path "*.vcf" , emit: vcf
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path "*.csv" , emit: stats
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path "*.phylip" , emit: phylip
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path "*.recombination_predictions.embl" , emit: embl_predicted
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path "*.branch_base_reconstruction.embl", emit: embl_branch
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path "*.final_tree.tre" , emit: tree
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path "*.node_labelled.final_tree.tre" , emit: tree_labelled
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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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"""
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run_gubbins.py \\
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--threads $task.cpus \\
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$options.args \\
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$alignment
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echo \$(run_gubbins.py --version 2>&1) > ${software}.version.txt
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"""
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}
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61
software/gubbins/meta.yml
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61
software/gubbins/meta.yml
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name: gubbins
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description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies
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loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the
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putative point mutations outside of these regions.
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keywords:
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- recombination
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- alignment
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tools:
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- gubbins:
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description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
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homepage: https://sanger-pathogens.github.io/gubbins/
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documentation: https://sanger-pathogens.github.io/gubbins/
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input:
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- alignment:
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type: file
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description: fasta alignment file
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pattern: "*.{fasta,fas,fa,aln}"
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output:
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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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- fasta:
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type: file
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description: Filtered variant alignment in fasta format
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pattern: "*.{fasta}"
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- embl_predicted:
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type: file
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description: Recombination predictions in embl format
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pattern: "*.{recombination_predictions.embl}"
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- gff:
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type: file
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description: Recombination predictions in gff format
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pattern: "*.{gff}"
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- embl_branch:
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type: file
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description: Branch base reconstruction
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pattern: "*.{branch_base_reconstruction.embl}"
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- vcf:
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type: file
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description: SNP distribution
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pattern: "*.{vcf}"
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- stats:
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type: file
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description: Per branch statistics
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pattern: "*.{csv}"
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- phylip:
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type: file
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description: Filtered variant alignment in phylip format
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pattern: "*.{phylip}"
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- tree:
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type: file
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description: Recombination removed RAxML phylogenetic tree
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pattern: "*.{final_tree.tre}"
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- tree_labelled:
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type: file
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description: Recombination removed RAxML phylogenetic tree (nodes labelled)
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pattern: "*.{node_labelled.final_tree.tre}"
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authors:
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- "@avantonder"
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@ -246,6 +246,10 @@ gffread:
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- software/gffread/**
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- tests/software/gffread/**
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gubbins:
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- software/gubbins/**
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- tests/software/gubbins/**
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gunzip:
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- software/gunzip/**
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- tests/software/gunzip/**
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kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
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test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
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test_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/test.fas"
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}
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'illumina' {
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test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"
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8
tests/data/genomics/sarscov2/genome/alignment/test.fas
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8
tests/data/genomics/sarscov2/genome/alignment/test.fas
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11
tests/software/gubbins/main.nf
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11
tests/software/gubbins/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GUBBINS } from '../../../software/gubbins/main.nf' addParams( options: [:] )
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workflow test_gubbins {
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input = file(params.test_data['sarscov2']['genome']['test_fas'], checkIfExists: true)
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GUBBINS ( input )
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}
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23
tests/software/gubbins/test.yml
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23
tests/software/gubbins/test.yml
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- name: gubbins
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command: nextflow run ./tests/software/gubbins -entry test_gubbins -c tests/config/nextflow.config
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tags:
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- gubbins
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files:
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- path: output/gubbins/test.filtered_polymorphic_sites.fasta
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md5sum: c9dff2294307eb2200a6e19efce47796
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- path: output/gubbins/test.recombination_predictions.embl
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/gubbins/test.recombination_predictions.gff
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md5sum: a2ca9c119674f4d121a8f78e4078fe05
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- path: output/gubbins/test.branch_base_reconstruction.embl
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/gubbins/test.summary_of_snp_distribution.vcf
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md5sum: afee50e92fb919a5df487fbda0b9dbb5
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- path: output/gubbins/test.per_branch_statistics.csv
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md5sum: 0f364b5e0b01a6be9b6a4407658ab25f
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- path: output/gubbins/test.filtered_polymorphic_sites.phylip
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md5sum: 85db9d0896cfec34a73641496b7498bb
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- path: output/gubbins/test.final_tree.tre
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md5sum: dce7164a0c69bb3d642a419907364aa3
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- path: output/gubbins/test.node_labelled.final_tree.tre
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md5sum: beef5ce05aca4598bb3f42caf126e045
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