mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
46 lines
1.5 KiB
Text
46 lines
1.5 KiB
Text
process UNICYCLER {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' :
|
|
'quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3' }"
|
|
|
|
input:
|
|
tuple val(meta), path(shortreads), path(longreads)
|
|
|
|
output:
|
|
tuple val(meta), path('*.scaffolds.fa.gz'), emit: scaffolds
|
|
tuple val(meta), path('*.assembly.gfa.gz'), emit: gfa
|
|
tuple val(meta), path('*.log') , emit: log
|
|
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 short_reads = shortreads ? ( meta.single_end ? "-s $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" ) : ""
|
|
def long_reads = longreads ? "-l $longreads" : ""
|
|
"""
|
|
unicycler \\
|
|
--threads $task.cpus \\
|
|
$args \\
|
|
$short_reads \\
|
|
$long_reads \\
|
|
--out ./
|
|
|
|
mv assembly.fasta ${prefix}.scaffolds.fa
|
|
gzip -n ${prefix}.scaffolds.fa
|
|
mv assembly.gfa ${prefix}.assembly.gfa
|
|
gzip -n ${prefix}.assembly.gfa
|
|
mv unicycler.log ${prefix}.unicycler.log
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
unicycler: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|