nf-core_modules/modules/msisensor/scan/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

42 lines
1.4 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } 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 "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
msisensor \\
scan \\
-d $fasta \\
-o ${prefix}.msisensor_scan.tab \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
END_VERSIONS
"""
}