Add hamronization/deeparg (#1364)

* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add when condition

* Apply suggestions from code review

* Update modules/hamronization/deeparg/meta.yml
This commit is contained in:
James A. Fellows Yates 2022-03-02 13:04:22 +01:00 committed by GitHub
parent 8e5eaf1fa4
commit 4983f77796
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7 changed files with 139 additions and 1 deletions

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@ -0,0 +1,44 @@
process HAMRONIZATION_DEEPARG {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
input:
tuple val(meta), path(report)
val(format)
val(software_version)
val(reference_db_version)
output:
tuple val(meta), path("*.json"), optional: true, emit: json
tuple val(meta), path("*.tsv") , optional: true, emit: tsv
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
hamronize \\
deeparg \\
${report} \\
$args \\
--format ${format} \\
--analysis_software_version ${software_version} \\
--reference_database_version ${reference_db_version} \\
--input_file_name ${prefix} \\
> ${prefix}.${format}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
END_VERSIONS
"""
}

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@ -0,0 +1,60 @@
name: hamronization_deeparg
description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification
keywords:
- amr
- antimicrobial resistance
- reporting
- deeparg
tools:
- hamronization:
description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
tool_dev_url: https://github.com/pha4ge/hAMRonization
doi: ""
licence: ['GNU Lesser General Public v3 (LGPL v3)']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- report:
type: file
description: Output .mapping.ARG file from DeepARG
pattern: "*.mapping.ARG"
- format:
type: value
description: Type of report file to be produced
pattern: "tsv|json"
- software_version:
type: value
description: Version of DeepARG used
pattern: "[0-9].[0-9].[0-9]"
- reference_db_version:
type: value
description: Database version of DeepARG used
pattern: "[0-9]"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- json:
type: file
description: hAMRonised report in JSON format
pattern: "*.json"
- tsv:
type: file
description: hAMRonised report in TSV format
pattern: "*.json"
authors:
- "@jfy133"

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@ -752,6 +752,10 @@ gunzip:
- modules/gunzip/**
- tests/modules/gunzip/**
hamronization/deeparg:
- modules/hamronization/deeparg/**
- tests/modules/hamronization/deeparg/**
hicap:
- modules/hicap/**
- tests/modules/hicap/**

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@ -68,7 +68,7 @@ params {
test_computematrix_mat_gz = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
test_bcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf"
test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
@ -321,6 +321,8 @@ params {
'genome' {
genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
}
'illumina' {
test1_contigs_fa_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"

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@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
workflow test_hamronization_deeparg {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
]
HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )
}

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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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@ -0,0 +1,8 @@
- name: hamronization deeparg test_hamronization_deeparg
command: nextflow run tests/modules/hamronization/deeparg -entry test_hamronization_deeparg -c tests/config/nextflow.config
tags:
- hamronization
- hamronization/deeparg
files:
- path: output/hamronization/test.tsv
md5sum: 3c315605aca0c5964796bb5fd4cdd522