nf-core_modules/software/bowtie2/build/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BOWTIE2_BUILD {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2=py38h1c8e9b9_1' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
} else {
container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
}
input:
path fasta
output:
path 'bowtie2' , emit: index
path '*.version.txt', emit: version
script:
def software = getSoftwareName(task.process)
"""
mkdir bowtie2
bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
"""
}