nf-core_modules/modules/graphmap2/index/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GRAPHMAP2_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:['']) }
conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0"
} else {
container "quay.io/biocontainers/graphmap:0.6.3--he513fc3_0"
}
input:
path fasta
output:
path "*.gmidx" , emit: index
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
"""
graphmap2 \\
align \\
-t $task.cpus \\
-I \\
$options.args \\
-r $fasta
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
"""
}