mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 22:23:09 +00:00
60 lines
2.4 KiB
Text
60 lines
2.4 KiB
Text
|
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
|
||
|
|
"""
|
||
|
|
}
|