nf-core_modules/modules/genmap/mappability/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

43 lines
1.4 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GENMAP_MAPPABILITY {
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), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1"
} else {
container "quay.io/biocontainers/genmap:1.3.0--h1b792b2_1"
}
input:
path index
output:
path "*.wig" , optional:true, emit: wig
path "*.bedgraph" , optional:true, emit: bedgraph
path "*.txt" , optional:true, emit: txt
path "versions.yml" , emit: versions
script:
"""
genmap \\
map \\
$options.args \\
-I $index \\
-O mappability
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
END_VERSIONS
"""
}