nf-core_modules/software/bismark/genomepreparation/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process BISMARK_GENOMEPREPARATION {
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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::bismark=0.23.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
} else {
container "quay.io/biocontainers/bismark:0.23.0--0"
}
input:
path fasta, stageAs: "BismarkIndex/*"
output:
path "BismarkIndex" , emit: index
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
bismark_genome_preparation \\
$options.args \\
BismarkIndex
echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
"""
}