mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
0337916f8a
* Initial work on yara module * Adding in index basics * Updated the index stuff * Adding in proper tests * Fix editorconfig * Odd paths * that should do it * Fix tests * Fix tests * FFS * Once more * Mapping is not deterministic
48 lines
1.9 KiB
Text
48 lines
1.9 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process YARA_MAPPER {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.12" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0"
|
|
} else {
|
|
container "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
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
|
|
if(meta.single_end) {
|
|
"""
|
|
yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara $reads | samtools view -@ ${task.cpus} -hb -F4 > ${prefix}.mapped.bam
|
|
|
|
echo \$(yara_mapper --help 2>&1) > ${software}.version.txt
|
|
"""
|
|
} else {
|
|
"""
|
|
yara_mapper $options.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 > ${prefix}_1.mapped.bam
|
|
samtools view -@ ${task.cpus} -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
|
|
echo \$(yara_mapper --version 2>&1) | grep -e "yara_mapper version:" | sed 's/yara_mapper version: //g' > ${software}.version.txt
|
|
"""
|
|
}
|
|
|
|
}
|