nf-core_modules/software/bowtie/align/main.nf
2020-12-08 13:40:32 +01:00

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// 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
"""
}