nf-core_modules/modules/metaphlan3/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process METAPHLAN3 {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0"
} else {
container "quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0"
}
input:
tuple val(meta), path(input)
path metaphlan_db
output:
tuple val(meta), path("*_profile.txt") , emit: profile
tuple val(meta), path("*.biom") , emit: biom
tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
"""
metaphlan \\
--nproc $task.cpus \\
$input_type \\
$input_data \\
$options.args \\
$bowtie2_out \\
--bowtie2db ${metaphlan_db} \\
--biom ${prefix}.biom \\
--output_file ${prefix}_profile.txt
echo \$(metaphlan --version 2>&1) | awk '{print \$3}' > ${software}.version.txt
"""
}