nf-core_modules/modules/minimap2/index/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 MINIMAP2_INDEX {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:['']) }
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conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
} else {
container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
}
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input:
path fasta
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output:
path "*.mmi" , emit: index
path "versions.yml" , emit: versions
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script:
"""
minimap2 \\
-t $task.cpus \\
-d ${fasta.baseName}.mmi \\
$options.args \\
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$fasta
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(minimap2 --version 2>&1)
END_VERSIONS
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"""
}