add module hamronization/amrfinderplus (#1888)

* add module hamronization/amrfinderplus

* deleted comments

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/hamronization/amrfinderplus/main.nf

@@ -0,0 +1,44 @@
+
+process HAMRONIZATION_AMRFINDERPLUS {
+    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 \\
+        amrfinderplus \\
+        ${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
+    """
+}

modules/hamronization/amrfinderplus/meta.yml

@@ -0,0 +1,61 @@
+name: "hamronization_amrfinderplus"
+description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification.
+keywords:
+  - amr
+  - antimicrobial resistance
+  - arg
+  - antimicrobial resistance genes
+  - reporting
+  - amrfinderplus
+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"
+      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 file from AMRfinderPlus
+      pattern: "*.tsv"
+  - format:
+      type: value
+      description: Type of report file to be produced
+      pattern: "tsv|json"
+  - software_version:
+      type: value
+      description: Version of AMRfinder used
+      pattern: "[0-9].[0-9].[0-9]"
+  - reference_db_version:
+      type: value
+      description: Database version of ncbi_AMRfinder used
+      pattern: "[0-9]-[0-9]-[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: "*.tsv"
+
+authors:
+  - "@louperelo"

tests/config/pytest_modules.yml

@@ -1023,6 +1023,10 @@ gunzip:
   - modules/gunzip/**
   - tests/modules/gunzip/**
 
+hamronization/amrfinderplus:
+  - modules/hamronization/amrfinderplus/**
+  - tests/modules/hamronization/amrfinderplus/**
+
 hamronization/deeparg:
   - modules/hamronization/deeparg/**
   - tests/modules/hamronization/deeparg/**

tests/modules/hamronization/amrfinderplus/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+include { HAMRONIZATION_AMRFINDERPLUS } from '../../../../modules/hamronization/amrfinderplus/main.nf'
+
+workflow test_hamronization_amrfinderplus {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true)
+    ]
+
+    HAMRONIZATION_AMRFINDERPLUS ( input, 'tsv', '3.10.30', '2022-05-26.1' )
+}

tests/modules/hamronization/amrfinderplus/nextflow.config

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

tests/modules/hamronization/amrfinderplus/test.yml

@@ -0,0 +1,8 @@
+- name: hamronization amrfinderplus test_hamronization_amrfinderplus
+  command: nextflow run ./tests/modules/hamronization/amrfinderplus -entry test_hamronization_amrfinderplus -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/amrfinderplus/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/amrfinderplus
+  files:
+    - path: output/hamronization/test.tsv
+      md5sum: 6ed7f74659df7bce285ca80fd531e138