Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>master
James A. Fellows Yates
2 years ago
committed by
GitHub
parent
1780cf9bcf
commit
daab0a77dd
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process HAMRONIZATION_FARGENE {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
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'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_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 ?: "${meta.id}"
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"""
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hamronize \\
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fargene \\
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${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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--input_file_name ${prefix} \\
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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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name: "hamronization_fargene"
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description: Tool to convert and summarize fARGene 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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- arg
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- antimicrobial resistance genes
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- reporting
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- fARGene
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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/"
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documentation: "https://github.com/pha4ge/hAMRonization/"
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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 .txt file from fARGene
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pattern: "*.txt"
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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 fARGene 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 fARGene used
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pattern: "[0-9].[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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- "@jfy133"
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@ -0,0 +1,19 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GUNZIP } from '../../../modules/gunzip/main.nf'
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include { FARGENE } from '../../../modules/fargene/main.nf'
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include { HAMRONIZATION_FARGENE } from '../../../../modules/hamronization/fargene/main.nf'
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workflow test_hamronization_fargene {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
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hmm_model = 'class_a'
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GUNZIP ( input )
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FARGENE ( GUNZIP.out.gunzip, hmm_model )
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HAMRONIZATION_FARGENE ( FARGENE.out.hmm, 'tsv', '0.1', '0.1' )
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}
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@ -0,0 +1,5 @@
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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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@ -0,0 +1,7 @@
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- name: hamronization fargene test_hamronization_fargene
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command: nextflow run ./tests/modules/hamronization/fargene -entry test_hamronization_fargene -c ./tests/config/nextflow.config -c ./tests/modules/hamronization/fargene/nextflow.config
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tags:
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- hamronization
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- hamronization/fargene
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files:
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- path: output/hamronization/test.tsv
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@ -1,12 +1,12 @@
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- name: hamronization summarize test_hamronization_summarize
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command: nextflow run ./tests/modules/hamronization/summarize -entry test_hamronization_summarize -c ./tests/config/nextflow.config -c ./tests/modules/hamronization/summarize/nextflow.config
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tags:
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- hamronization/summarize
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- hamronization
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- hamronization/summarize
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files:
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- path: output/hamronization/hamronization_combined_report.json
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md5sum: 1623b6cc3b213208a425e023edd94691
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md5sum: ab0c899664398193a25a699b92f960b9
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- path: output/hamronization/test.tsv
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md5sum: 3c315605aca0c5964796bb5fd4cdd522
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md5sum: e886d665bf9fc266be8193859863d2f4
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- path: output/hamronization/test2.tsv
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md5sum: 453f38502e35261a50a0849dca34f05b
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md5sum: 2d94ecb8be8d9036877e47a81ae92a41
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