nf-core_modules/modules/merqury/main.nf

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process MERQURY {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::merqury=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1':
'quay.io/biocontainers/merqury:1.3--hdfd78af_1' }"
input:
tuple val(meta), path(meryl_db), path(assembly)
output:
tuple val(meta), path("*_only.bed") , emit: assembly_only_kmers_bed
tuple val(meta), path("*_only.wig") , emit: assembly_only_kmers_wig
tuple val(meta), path("*.completeness.stats"), emit: stats
tuple val(meta), path("*.dist_only.hist") , emit: dist_hist
tuple val(meta), path("*.spectra-cn.fl.png") , emit: spectra_cn_fl_png
tuple val(meta), path("*.spectra-cn.hist") , emit: spectra_cn_hist
tuple val(meta), path("*.spectra-cn.ln.png") , emit: spectra_cn_ln_png
tuple val(meta), path("*.spectra-cn.st.png") , emit: spectra_cn_st_png
tuple val(meta), path("*.spectra-asm.fl.png"), emit: spectra_asm_fl_png
tuple val(meta), path("*.spectra-asm.hist") , emit: spectra_asm_hist
tuple val(meta), path("*.spectra-asm.ln.png"), emit: spectra_asm_ln_png
tuple val(meta), path("*.spectra-asm.st.png"), emit: spectra_asm_st_png
tuple val(meta), path("${prefix}.qv") , emit: assembly_qv
tuple val(meta), path("${prefix}.*.qv") , emit: scaffold_qv
tuple val(meta), path("*.hist.ploidy") , emit: read_ploidy
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
// def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = 1.3
"""
# Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
# Check for container variable initialisation script and source it.
if [ -f "/usr/local/env-activate.sh" ]; then
set +u # Otherwise, errors out because of various unbound variables
. "/usr/local/env-activate.sh"
set -u
fi
# limit meryl to use the assigned number of cores.
export OMP_NUM_THREADS=$task.cpus
merqury.sh \\
$meryl_db \\
$assembly \\
$prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
merqury: $VERSION
END_VERSIONS
"""
}