You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
40 lines
1.3 KiB
Plaintext
40 lines
1.3 KiB
Plaintext
process FILTLONG {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
|
|
'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(shortreads), path(longreads)
|
|
|
|
output:
|
|
tuple val(meta), path("*.fastq.gz"), emit: reads
|
|
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 ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
|
|
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
|
|
"""
|
|
filtlong \\
|
|
$short_reads \\
|
|
$args \\
|
|
$longreads \\
|
|
2> ${prefix}.log \\
|
|
| gzip -n > ${prefix}.fastq.gz
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
filtlong: \$( filtlong --version | sed -e "s/Filtlong v//g" )
|
|
END_VERSIONS
|
|
"""
|
|
}
|