mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
def options = initOptions(params.options)
|
||
|
|
|
||
|
|
process BOWTIE_ALIGN {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_high'
|
||
|
|
publishDir "${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::bowtie=1.3.0" : null)
|
||
|
|
container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(reads)
|
||
|
|
path index
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.sam") , emit: sam
|
||
|
|
tuple val(meta), path("*.out") , emit: log
|
||
|
|
path "bowtie.version.txt" , emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
|
index_array = index.collect()
|
||
|
|
index = index_array[0].baseName - ~/.\d$/
|
||
|
|
"""
|
||
|
|
bowtie $options.args \\
|
||
|
|
--threads $task.cpus \\
|
||
|
|
${index} \\
|
||
|
|
-q ${reads} \\
|
||
|
|
--un ${prefix}.unAl > ${prefix}.sam 2> ${prefix}.out
|
||
|
|
bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|