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

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process MASHTREE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0' :
'quay.io/biocontainers/mashtree:1.2.0--pl526h516909a_0' }"
input:
tuple val(meta), path(seqs)
output:
tuple val(meta), path("*.dnd"), emit: tree
tuple val(meta), path("*.tsv"), emit: matrix
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}"
"""
mashtree \\
$args \\
--numcpus $task.cpus \\
--outmatrix ${prefix}.tsv \\
--outtree ${prefix}.dnd \\
$seqs
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mashtree: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' )
END_VERSIONS
"""
}