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

modules/hamronization/deeparg/main.nf

@@ -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
+    """
+}

modules/hamronization/deeparg/meta.yml

@@ -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"

tests/config/pytest_modules.yml

@@ -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/**

tests/config/test_data.config

@@ -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"

tests/modules/hamronization/deeparg/main.nf

@@ -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'  )
+}

tests/modules/hamronization/deeparg/nextflow.config

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

tests/modules/hamronization/deeparg/test.yml

@@ -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