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

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BBMAP_INDEX {
tag "$fasta"
label 'process_long'
publishDir "${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::bbmap=38.92" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0"
} else {
container "quay.io/biocontainers/bbmap:38.92--he522d1c_0"
}
input:
path fasta
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output:
path 'ref' , emit: index
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path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
bbmap.sh \\
ref=${fasta} \\
$options.args \\
threads=$task.cpus \\
-Xmx${task.memory.toGiga()}g
echo \$(bbversion.sh) > ${software}.version.txt
"""
}