nf-core_modules/modules/yara/mapper/main.nf
Michael L Heuer 251015c8ba
Add samtools index to yara_mapper module (#1353)
* Add samtools index to yara_mapper module.

* samtools sort required for index

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-03-04 10:08:02 -05:00

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2.4 KiB
Text

process YARA_MAPPER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.12" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' :
'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-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
"""
}
}