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.
44 lines
1.4 KiB
Plaintext
44 lines
1.4 KiB
Plaintext
process BBMAP_BBDUK {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda "bioconda::bbmap=39.01"
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0':
|
|
'quay.io/biocontainers/bbmap:39.01--h5c4e2a8_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path contaminants
|
|
|
|
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 ?: "${meta.id}"
|
|
def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
|
|
def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
|
|
def contaminants_fa = contaminants ? "ref=$contaminants" : ''
|
|
"""
|
|
maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
|
|
bbduk.sh \\
|
|
-Xmx\$maxmem \\
|
|
$raw \\
|
|
$trimmed \\
|
|
threads=$task.cpus \\
|
|
$args \\
|
|
$contaminants_fa \\
|
|
&> ${prefix}.bbduk.log
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
|
|
END_VERSIONS
|
|
"""
|
|
}
|