nf-core_modules/software/msisensor/scan/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process MSISENSOR_SCAN {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
} else {
container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
}
input:
tuple val(meta), path(fasta)
output:
tuple (val(meta), path("*.tab"), emit: txt)
path ("*.version.txt" , emit: version)
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
msisensor \\
scan \\
-d $fasta \\
-o ${prefix}.msisensor_scan.tab \\
$options.args
echo \$(msisensor 2>&1) | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p' > ${software}.version.txt
"""
}