mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
897c33d5da
* Fix typo * update version to 1.15.1 * Fix md5sums * update mulled containers * update md5sums * update md5sums
65 lines
2.4 KiB
Text
65 lines
2.4 KiB
Text
process YARA_MAPPER {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' :
|
|
'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path index
|
|
|
|
output:
|
|
tuple val(meta), path("*.mapped.bam"), emit: bam
|
|
tuple val(meta), path("*.mapped.bam.bai"), emit: bai
|
|
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}"
|
|
if (meta.single_end) {
|
|
"""
|
|
yara_mapper \\
|
|
$args \\
|
|
-t $task.cpus \\
|
|
-f bam \\
|
|
${index}/yara \\
|
|
$reads | samtools view -@ $task.cpus -hb -F4 | samtools sort -@ $task.cpus > ${prefix}.mapped.bam
|
|
|
|
samtools index -@ $task.cpus ${prefix}.mapped.bam
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
} else {
|
|
"""
|
|
yara_mapper \\
|
|
$args \\
|
|
-t $task.cpus \\
|
|
-f bam \\
|
|
${index}/yara \\
|
|
${reads[0]} \\
|
|
${reads[1]} > output.bam
|
|
|
|
samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_1.mapped.bam
|
|
samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_2.mapped.bam
|
|
|
|
samtools index -@ $task.cpus ${prefix}_1.mapped.bam
|
|
samtools index -@ $task.cpus ${prefix}_2.mapped.bam
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|
|
}
|