mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process MINIA {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::minia=3.2.4" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0"
|
|
} else {
|
|
container "quay.io/biocontainers/minia:3.2.4--he513fc3_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
|
|
output:
|
|
tuple val(meta), path('*.contigs.fa'), emit: contigs
|
|
tuple val(meta), path('*.unitigs.fa'), emit: unitigs
|
|
tuple val(meta), path('*.h5') , emit: h5
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def read_list = reads.join(",")
|
|
"""
|
|
echo "${read_list}" | sed 's/,/\\n/g' > input_files.txt
|
|
minia \\
|
|
$options.args \\
|
|
-nb-cores $task.cpus \\
|
|
-in input_files.txt \\
|
|
-out $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
|
|
END_VERSIONS
|
|
"""
|
|
}
|