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37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
process ISMAPPER {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' :
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'quay.io/biocontainers/ismapper:2.0.2--pyhdfd78af_1' }"
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input:
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tuple val(meta), path(reads), path(reference), path(query)
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output:
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tuple val(meta), 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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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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ismap \\
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$args \\
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--t $task.cpus \\
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--output_dir results \\
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--queries $query \\
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--reference $reference \\
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--reads $reads
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ismapper: \$( echo \$( ismap --version 2>&1 ) | sed 's/^.*ismap //' )
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END_VERSIONS
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"""
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}
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