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39 lines
1,019 B
Text
39 lines
1,019 B
Text
process MALTEXTRACT {
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::hops=0.35" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
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'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"
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input:
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path rma6
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path taxon_list
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path ncbi_dir
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output:
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path "results" , emit: results
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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MaltExtract \\
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-Xmx${task.memory.toGiga()}g \\
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-p $task.cpus \\
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-i ${rma6.join(' ')} \\
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-t $taxon_list \\
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-r $ncbi_dir \\
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-o results/ \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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maltextract: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//')
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END_VERSIONS
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"""
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}
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