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Add module hamronization/abricate
(#1925)
* Add hamronization/abricate * Update input pattern in meta.yml * Update location of hamronization test data * Apply suggestions from code review
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8 changed files with 141 additions and 3 deletions
43
modules/hamronization/abricate/main.nf
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43
modules/hamronization/abricate/main.nf
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process HAMRONIZATION_ABRICATE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
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'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
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input:
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tuple val(meta), path(report)
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val(format)
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val(software_version)
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val(reference_db_version)
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output:
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tuple val(meta), path("*.json"), optional: true, emit: json
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tuple val(meta), path("*.tsv") , optional: true, emit: tsv
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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hamronize \\
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abricate \\
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${report} \\
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$args \\
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--format ${format} \\
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--analysis_software_version ${software_version} \\
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--reference_database_version ${reference_db_version} \\
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> ${prefix}.${format}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
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END_VERSIONS
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"""
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}
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60
modules/hamronization/abricate/meta.yml
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60
modules/hamronization/abricate/meta.yml
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name: "hamronization_abricate"
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description: Tool to convert and summarize ABRicate outputs using the hAMRonization specification
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keywords:
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- amr
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- antimicrobial resistance
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- reporting
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- abricate
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tools:
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- "hamronization":
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description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
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homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
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documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
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tool_dev_url: "https://github.com/pha4ge/hAMRonization"
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doi: ""
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licence: "['GNU Lesser General Public v3 (LGPL 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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- report:
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type: file
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description: Output TSV or CSV file from ABRicate
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pattern: "*.{csv,tsv}"
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- format:
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type: value
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description: Type of report file to be produced
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pattern: "tsv|json"
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- software_version:
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type: value
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description: Version of ABRicate used
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pattern: "[0-9].[0-9].[0-9]"
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- reference_db_version:
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type: value
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description: Database version of ABRicate used
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pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]"
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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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- json:
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type: file
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description: hAMRonised report in JSON format
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pattern: "*.json"
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- tsv:
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type: file
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description: hAMRonised report in TSV format
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pattern: "*.json"
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authors:
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- "@jasmezz"
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@ -1035,6 +1035,10 @@ gvcftools/extractvariants:
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- modules/gvcftools/extractvariants/**
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- tests/modules/gvcftools/extractvariants/**
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hamronization/abricate:
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- modules/hamronization/abricate/**
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- tests/modules/hamronization/abricate/**
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hamronization/amrfinderplus:
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- modules/hamronization/amrfinderplus/**
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- tests/modules/hamronization/amrfinderplus/**
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@ -369,10 +369,13 @@ params {
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genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
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genome_gbff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
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genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
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genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
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genome_gff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz"
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genome_gff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz"
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}
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'hamronization' {
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genome_abricate_tsv = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv"
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genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG"
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}
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'illumina' {
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test1_contigs_fa_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
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test1_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz"
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15
tests/modules/hamronization/abricate/main.nf
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15
tests/modules/hamronization/abricate/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { HAMRONIZATION_ABRICATE } from '../../../../modules/hamronization/abricate/main.nf'
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workflow test_hamronization_abricate {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true),
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]
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HAMRONIZATION_ABRICATE ( input, 'tsv', '1.0.1', '2021-Mar-27' )
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}
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5
tests/modules/hamronization/abricate/nextflow.config
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5
tests/modules/hamronization/abricate/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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8
tests/modules/hamronization/abricate/test.yml
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8
tests/modules/hamronization/abricate/test.yml
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- name: hamronization abricate test_hamronization_abricate
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command: nextflow run ./tests/modules/hamronization/abricate -entry test_hamronization_abricate -c ./tests/config/nextflow.config -c ./tests/modules/hamronization/abricate/nextflow.config
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tags:
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- hamronization/abricate
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- hamronization
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files:
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- path: output/hamronization/test.tsv
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md5sum: 1c774f024872da954126d0ff77b77ea7
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@ -8,7 +8,7 @@ workflow test_hamronization_deeparg {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
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file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
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]
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HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )
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