mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
70 lines
2.4 KiB
Text
70 lines
2.4 KiB
Text
process MEGAHIT {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' :
|
|
'quay.io/biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
|
|
output:
|
|
tuple val(meta), path("megahit_out/*.contigs.fa.gz") , emit: contigs
|
|
tuple val(meta), path("megahit_out/intermediate_contigs/k*.contigs.fa.gz") , emit: k_contigs
|
|
tuple val(meta), path("megahit_out/intermediate_contigs/k*.addi.fa.gz") , emit: addi_contigs
|
|
tuple val(meta), path("megahit_out/intermediate_contigs/k*.local.fa.gz") , emit: local_contigs
|
|
tuple val(meta), path("megahit_out/intermediate_contigs/k*.final.contigs.fa.gz"), emit: kfinal_contigs
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def args2 = task.ext.args2 ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
if (meta.single_end) {
|
|
"""
|
|
megahit \\
|
|
-r ${reads} \\
|
|
-t $task.cpus \\
|
|
$args \\
|
|
--out-prefix $prefix
|
|
|
|
pigz \\
|
|
--no-name \\
|
|
-p $task.cpus \\
|
|
$args2 \\
|
|
megahit_out/*.fa \\
|
|
megahit_out/intermediate_contigs/*.fa
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
|
|
END_VERSIONS
|
|
"""
|
|
} else {
|
|
"""
|
|
megahit \\
|
|
-1 ${reads[0]} \\
|
|
-2 ${reads[1]} \\
|
|
-t $task.cpus \\
|
|
$args \\
|
|
--out-prefix $prefix
|
|
|
|
pigz \\
|
|
--no-name \\
|
|
-p $task.cpus \\
|
|
$args2 \\
|
|
megahit_out/*.fa \\
|
|
megahit_out/intermediate_contigs/*.fa
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|
|
}
|