nf-core_modules/modules/metaphlan3/main.nf

45 lines
1.8 KiB
Text

process METAPHLAN3 {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
'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 "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_type = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" : ("$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 \\
$args \\
$bowtie2_out \\
--bowtie2db ${metaphlan_db} \\
--biom ${prefix}.biom \\
--output_file ${prefix}_profile.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
END_VERSIONS
"""
}