add module for rgi (#1321)

* add module for rgi

* fix extension

* fix test yaml

* Update main.nf

* Update main.nf
This commit is contained in:
Robert A. Petit III 2022-02-18 17:23:44 -07:00 committed by GitHub
parent cab399507b
commit 8055c5d1c3
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6 changed files with 120 additions and 0 deletions

37
modules/rgi/main/main.nf Normal file
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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
"""
}

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modules/rgi/main/meta.yml Normal file
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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"

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

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#!/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 )
}

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

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- 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