2021-09-21 18:57:27 +00:00
|
|
|
// Import generic module functions
|
2021-09-27 08:41:24 +00:00
|
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
2021-09-21 18:57:27 +00:00
|
|
|
|
|
|
|
params.options = [:]
|
|
|
|
options = initOptions(params.options)
|
|
|
|
|
|
|
|
process MALTEXTRACT {
|
|
|
|
|
|
|
|
label 'process_medium'
|
|
|
|
publishDir "${params.outdir}",
|
|
|
|
mode: params.publish_dir_mode,
|
|
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
|
|
|
|
conda (params.enable_conda ? "bioconda::hops=0.35" : null)
|
|
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
|
|
container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
|
|
|
|
} else {
|
|
|
|
container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
|
|
|
|
}
|
|
|
|
|
|
|
|
input:
|
|
|
|
path rma6
|
|
|
|
path taxon_list
|
|
|
|
path ncbi_dir
|
|
|
|
|
|
|
|
output:
|
|
|
|
path "results" , emit: results
|
2021-09-27 08:41:24 +00:00
|
|
|
path "versions.yml" , emit: version
|
2021-09-21 18:57:27 +00:00
|
|
|
|
|
|
|
script:
|
|
|
|
def software = getSoftwareName(task.process)
|
|
|
|
"""
|
|
|
|
MaltExtract \\
|
|
|
|
-Xmx${task.memory.toGiga()}g \\
|
|
|
|
-p $task.cpus \\
|
|
|
|
-i ${rma6.join(' ')} \\
|
|
|
|
-t $taxon_list \\
|
|
|
|
-r $ncbi_dir \\
|
|
|
|
-o results/ \\
|
|
|
|
$options.args
|
|
|
|
|
2021-09-27 08:41:24 +00:00
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
|
|
${getProcessName(task.process)}:
|
|
|
|
${getSoftwareName(task.process)}: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//')
|
|
|
|
END_VERSIONS
|
2021-09-21 18:57:27 +00:00
|
|
|
"""
|
|
|
|
}
|