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