add module for rgi (#1321)

* add module for rgi

* fix extension

* fix test yaml

* Update main.nf

* Update main.nf

modules/rgi/main/main.nf

@@ -0,0 +1,37 @@
+process RGI_MAIN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2':
+        'quay.io/biocontainers/rgi:5.2.1--pyha8f3691_2' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    tuple val(meta), path("*.txt") , 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}"
+    """
+    rgi \\
+        main \\
+        $args \\
+        --num_threads $task.cpus \\
+        --output_file $prefix \\
+        --input_sequence $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(rgi main --version)
+    END_VERSIONS
+    """
+}

modules/rgi/main/meta.yml

@@ -0,0 +1,47 @@
+name: rgi_main
+description: Predict antibiotic resistance from protein or nucleotide data
+keywords:
+  - bacteria
+  - fasta
+  - antibiotic resistance
+tools:
+  - rgi:
+      description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website
+      homepage: https://card.mcmaster.ca
+      documentation: https://github.com/arpcard/rgi
+      tool_dev_url: https://github.com/arpcard/rgi
+      doi: "10.1093/nar/gkz935"
+      licence: ['https://card.mcmaster.ca/about']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Nucleotide or protein sequences in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+
+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: JSON formatted file with RGI results
+      pattern: "*.{json}"
+  - tsv:
+      type: file
+      description: Tab-delimited file with RGI results
+      pattern: "*.{txt}"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -1261,6 +1261,10 @@ raxmlng:
   - modules/raxmlng/**
   - tests/modules/raxmlng/**
 
+rgi/main:
+  - modules/rgi/main/**
+  - tests/modules/rgi/main/**
+
 rmarkdownnotebook:
   - modules/rmarkdownnotebook/**
   - tests/modules/rmarkdownnotebook/**

tests/modules/rgi/main/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RGI_MAIN } from '../../../../modules/rgi/main/main.nf'
+
+workflow test_rgi_main {
+
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    RGI_MAIN ( input )
+}

tests/modules/rgi/main/nextflow.config

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

tests/modules/rgi/main/test.yml

@@ -0,0 +1,12 @@
+- name: rgi main
+  command: nextflow run ./tests/modules/rgi/main -entry test_rgi_main -c ./tests/config/nextflow.config -c ./tests/modules/rgi/main/nextflow.config
+  tags:
+    - rgi
+    - rgi/main
+  files:
+    - path: output/rgi/test.json
+      contains: ["NZ_LS483480", "orf_end", "perc_identity", "Pulvomycin"]
+    - path: output/rgi/test.txt
+      contains: ["NZ_LS483480", "ORF_ID", "Model_type", "Pulvomycin"]
+    - path: output/rgi/versions.yml
+      md5sum: 614a45d9d59680d4e743498773cf830a