mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
50 lines
2.2 KiB
Text
50 lines
2.2 KiB
Text
// 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=3.0.10" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.10--pyhb7b1952_0"
|
|
} else {
|
|
container "quay.io/biocontainers/metaphlan:3.0.10--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
|
|
"""
|
|
}
|