From 7f7f6bc913af85decaeba35827cea7943bf1042e Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Tue, 26 Jul 2022 12:55:53 +0200 Subject: [PATCH] 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 --- modules/hamronization/abricate/main.nf | 43 +++++++++++++ modules/hamronization/abricate/meta.yml | 60 +++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/config/test_data.config | 7 ++- tests/modules/hamronization/abricate/main.nf | 15 +++++ .../hamronization/abricate/nextflow.config | 5 ++ tests/modules/hamronization/abricate/test.yml | 8 +++ tests/modules/hamronization/deeparg/main.nf | 2 +- 8 files changed, 141 insertions(+), 3 deletions(-) create mode 100644 modules/hamronization/abricate/main.nf create mode 100644 modules/hamronization/abricate/meta.yml create mode 100644 tests/modules/hamronization/abricate/main.nf create mode 100644 tests/modules/hamronization/abricate/nextflow.config create mode 100644 tests/modules/hamronization/abricate/test.yml diff --git a/modules/hamronization/abricate/main.nf b/modules/hamronization/abricate/main.nf new file mode 100644 index 00000000..0bf34384 --- /dev/null +++ b/modules/hamronization/abricate/main.nf @@ -0,0 +1,43 @@ +process HAMRONIZATION_ABRICATE { + 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 \\ + abricate \\ + ${report} \\ + $args \\ + --format ${format} \\ + --analysis_software_version ${software_version} \\ + --reference_database_version ${reference_db_version} \\ + > ${prefix}.${format} + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) + END_VERSIONS + """ +} diff --git a/modules/hamronization/abricate/meta.yml b/modules/hamronization/abricate/meta.yml new file mode 100644 index 00000000..11913e38 --- /dev/null +++ b/modules/hamronization/abricate/meta.yml @@ -0,0 +1,60 @@ +name: "hamronization_abricate" +description: Tool to convert and summarize ABRicate outputs using the hAMRonization specification +keywords: + - amr + - antimicrobial resistance + - reporting + - abricate +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 TSV or CSV file from ABRicate + pattern: "*.{csv,tsv}" + - format: + type: value + description: Type of report file to be produced + pattern: "tsv|json" + - software_version: + type: value + description: Version of ABRicate used + pattern: "[0-9].[0-9].[0-9]" + - reference_db_version: + type: value + description: Database version of ABRicate used + pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][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: + - "@jasmezz" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 3f971c62..adb06cc2 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1035,6 +1035,10 @@ gvcftools/extractvariants: - modules/gvcftools/extractvariants/** - tests/modules/gvcftools/extractvariants/** +hamronization/abricate: + - modules/hamronization/abricate/** + - tests/modules/hamronization/abricate/** + hamronization/amrfinderplus: - modules/hamronization/amrfinderplus/** - tests/modules/hamronization/amrfinderplus/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index ecb69f98..3e34f918 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -369,10 +369,13 @@ params { genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" genome_gbff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" - genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG" - genome_gff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" + genome_gff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" } + 'hamronization' { + genome_abricate_tsv = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv" + genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG" + } 'illumina' { test1_contigs_fa_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" test1_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" diff --git a/tests/modules/hamronization/abricate/main.nf b/tests/modules/hamronization/abricate/main.nf new file mode 100644 index 00000000..11182469 --- /dev/null +++ b/tests/modules/hamronization/abricate/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { HAMRONIZATION_ABRICATE } from '../../../../modules/hamronization/abricate/main.nf' + +workflow test_hamronization_abricate { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true), + ] + + HAMRONIZATION_ABRICATE ( input, 'tsv', '1.0.1', '2021-Mar-27' ) +} diff --git a/tests/modules/hamronization/abricate/nextflow.config b/tests/modules/hamronization/abricate/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/hamronization/abricate/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/hamronization/abricate/test.yml b/tests/modules/hamronization/abricate/test.yml new file mode 100644 index 00000000..032e4229 --- /dev/null +++ b/tests/modules/hamronization/abricate/test.yml @@ -0,0 +1,8 @@ +- name: hamronization abricate test_hamronization_abricate + command: nextflow run ./tests/modules/hamronization/abricate -entry test_hamronization_abricate -c ./tests/config/nextflow.config -c ./tests/modules/hamronization/abricate/nextflow.config + tags: + - hamronization/abricate + - hamronization + files: + - path: output/hamronization/test.tsv + md5sum: 1c774f024872da954126d0ff77b77ea7 diff --git a/tests/modules/hamronization/deeparg/main.nf b/tests/modules/hamronization/deeparg/main.nf index 9888bc42..3f674bbc 100644 --- a/tests/modules/hamronization/deeparg/main.nf +++ b/tests/modules/hamronization/deeparg/main.nf @@ -8,7 +8,7 @@ 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), + file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true), ] HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )