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add pirate module (#777)
* new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Robert A. Petit III
GitHub
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6 changed files with 286 additions and 0 deletions
78
modules/pirate/functions.nf
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78
modules/pirate/functions.nf
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@ -0,0 +1,78 @@
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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43
modules/pirate/main.nf
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43
modules/pirate/main.nf
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@ -0,0 +1,43 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process PIRATE {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1"
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} else {
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container "quay.io/biocontainers/pirate:1.0.4--hdfd78af_1"
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}
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input:
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tuple val(meta), path(gff)
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output:
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tuple val(meta), path("results/*") , emit: results
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tuple val(meta), path("results/core_alignment.fasta"), optional: true, emit: aln
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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PIRATE \\
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$options.args \\
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--threads $task.cpus \\
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--input ./ \\
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--output results/
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
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END_VERSIONS
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"""
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}
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47
modules/pirate/meta.yml
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47
modules/pirate/meta.yml
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@ -0,0 +1,47 @@
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name: pirate
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description: Pangenome toolbox for bacterial genomes
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keywords:
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- gff
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- pan-genome
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- alignment
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tools:
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- pirate:
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description: Pangenome analysis and threshold evaluation toolbox
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homepage: https://github.com/SionBayliss/PIRATE
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documentation: https://github.com/SionBayliss/PIRATE/wiki
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tool_dev_url: https://github.com/SionBayliss/PIRATE
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doi: "https://doi.org/10.1093/gigascience/giz119"
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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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- gff:
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type: file
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description: A set of GFF3 formatted files
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pattern: "*.{gff}"
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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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- 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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- results:
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type: directory
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description: Directory containing PIRATE result files
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pattern: "*/*"
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- aln:
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type: file
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description: Core-genome alignment produced by PIRATE (Optional)
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pattern: "*.{fasta}"
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authors:
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- "@rpetit3"
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@ -755,6 +755,10 @@ picard/sortsam:
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- modules/picard/sortsam/**
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- tests/modules/picard/sortsam/**
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pirate:
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- modules/pirate/**
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- tests/modules/pirate/**
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plasmidid:
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- modules/plasmidid/**
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- tests/modules/plasmidid/**
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16
tests/modules/pirate/main.nf
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16
tests/modules/pirate/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PIRATE } from '../../../modules/pirate/main.nf' addParams( options: [:] )
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workflow test_pirate {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000292685.gff", checkIfExists: true),
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file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000298385.gff", checkIfExists: true),
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file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_002849995.gff", checkIfExists: true) ]
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]
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PIRATE ( input )
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}
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98
tests/modules/pirate/test.yml
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98
tests/modules/pirate/test.yml
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@ -0,0 +1,98 @@
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- name: pirate test_pirate
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command: nextflow run tests/modules/pirate -entry test_pirate -c tests/config/nextflow.config
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tags:
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- pirate
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files:
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- path: output/pirate/results/PIRATE.gene_families.ordered.tsv
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contains: ['allele_name']
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- path: output/pirate/results/PIRATE.gene_families.tsv
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contains: ['allele_name']
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- path: output/pirate/results/PIRATE.genomes_per_allele.tsv
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contains: ['g0197']
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- path: output/pirate/results/PIRATE.log
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contains: ['PIRATE input options']
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- path: output/pirate/results/PIRATE.pangenome_summary.txt
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md5sum: 4551c291bc06b21f984f25c09329ed7d
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- path: output/pirate/results/PIRATE.unique_alleles.tsv
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contains: ['allele_name']
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- path: output/pirate/results/binary_presence_absence.fasta
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contains: ['GCF_000292685']
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- path: output/pirate/results/binary_presence_absence.nwk
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md5sum: 5b5d86bf97d97de37bb9db514abb7762
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- path: output/pirate/results/cluster_alleles.tab
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contains: ['g0001']
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- path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab
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md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
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- path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab
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md5sum: a24d6048b3074242bb558c7fa27a8b03
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- path: output/pirate/results/co-ords/GCF_002849995.co-ords.tab
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md5sum: 0c08228585f4fa95686e9b025e0fe9c1
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- path: output/pirate/results/genome2loci.tab
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md5sum: bbcea5bfcdcafe14a9aa7261c8e931b8
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- path: output/pirate/results/genome_list.txt
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md5sum: 6534b1635c258ad92b829077addc1ff5
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- path: output/pirate/results/link_clusters.log
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contains: ['parsing paralog file']
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- path: output/pirate/results/loci_list.tab
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/loci_paralog_categories.tab
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md5sum: 6404d2a32526a398f42d7da768a389bd
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- path: output/pirate/results/modified_gffs/GCF_000292685.gff
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md5sum: 2b73bda2f84dc634303dc90e641040ca
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- path: output/pirate/results/modified_gffs/GCF_000298385.gff
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md5sum: b1a9d6557d47e09249f08a7acdbbd618
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- path: output/pirate/results/modified_gffs/GCF_002849995.gff
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md5sum: 68532fc9bb639e6d83c731a069f60cf8
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- path: output/pirate/results/pan_sequences.fasta
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md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb
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- path: output/pirate/results/pangenome.connected_blocks.tsv
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contains: ['block_number']
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- path: output/pirate/results/pangenome.edges
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contains: ['g0259']
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- path: output/pirate/results/pangenome.gfa
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contains: ['g0001']
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- path: output/pirate/results/pangenome.order.tsv
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contains: ['g0172']
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- path: output/pirate/results/pangenome.reversed.tsv
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md5sum: b2396ce09a6e4178761eca6dc7f4434f
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- path: output/pirate/results/pangenome.syntenic_blocks.tsv
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contains: ['g0091']
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- path: output/pirate/results/pangenome.temp
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- path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
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md5sum: 9da25d27684bfcc5488987ab2d1fd3a1
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- path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
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contains: ['GCF_000298385_00081']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
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contains: ['GCF_000298385_00242']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
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contains: ['chaos']
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
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md5sum: 84668b6c65b57026a17a50b0edd02541
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto
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- path: output/pirate/results/pangenome_log.txt
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contains: ['Creating pangenome on amino acid']
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- path: output/pirate/results/paralog_clusters.tab
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contains: ['g0216']
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- path: output/pirate/results/representative_sequences.faa
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contains: ['representative_genome']
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- path: output/pirate/results/representative_sequences.ffn
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contains: ['representative_genome']
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- path: output/pirate/results/split_groups.log
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contains: ['g0213']
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