nf-core_modules/modules/motus/downloaddb/main.nf

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process MOTUS_DOWNLOADDB {
label 'process_low'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
input:
path motus_downloaddb_script
output:
path "db_mOTU/" , emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def software = "${motus_downloaddb_script.simpleName}_copy.py"
"""
## must copy script file to working directory,
## otherwise the reference_db will be download to bin folder
## other than current directory
cp $motus_downloaddb_script ${software}
python ${software} \\
$args \\
-t $task.cpus
## mOTUs version number is not available from command line.
## mOTUs save the version number in index database folder.
## mOTUs will check the database version is same version as exec version.
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
END_VERSIONS
"""
}