nf-core_modules/modules/minia/main.nf
2022-02-04 09:53:32 +01:00

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process MINIA {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::minia=3.2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.contigs.fa'), emit: contigs
tuple val(meta), path('*.unitigs.fa'), emit: unitigs
tuple val(meta), path('*.h5') , emit: h5
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def read_list = reads.join(",")
"""
echo "${read_list}" | sed 's/,/\\n/g' > input_files.txt
minia \\
$args \\
-nb-cores $task.cpus \\
-in input_files.txt \\
-out $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
END_VERSIONS
"""
}