nf-core_modules/software/yara/index/main.nf
2021-04-10 20:49:09 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process YARA_INDEX {
tag "$fasta"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::yara=1.0.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/yara:1.0.2--2"
} else {
container "quay.io/biocontainers/yara:1.0.2--2"
}
input:
path fasta
output:
path "yara", emit: index
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
mkdir yara
yara_indexer $fasta -o "yara"
mv *.{lf,rid,sa,txt}.* yara
cp $fasta yara/yara.fasta
echo \$(yara_indexer --help 2>&1) | grep -e "yara_indexer version:" | sed 's/yara_indexer version: //g' > ${software}.version.txt
"""
}