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

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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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:'index', meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0'
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} else {
container 'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0'
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}
input:
path fasta
output:
path 'bowtie2' , emit: index
path "versions.yml" , emit: versions
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script:
"""
mkdir bowtie2
bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
END_VERSIONS
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"""
}