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

@@ -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
+    """
+}

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"

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/**

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"

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' )
+}

tests/modules/hamronization/abricate/nextflow.config

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

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

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'  )