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38 lines
1 KiB
Text
38 lines
1 KiB
Text
process MINIMAP2_ALIGN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
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'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
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input:
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tuple val(meta), path(reads)
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path reference
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output:
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tuple val(meta), path("*.paf"), emit: paf
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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 ?: "${meta.id}"
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def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
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"""
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minimap2 \\
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$args \\
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-t $task.cpus \\
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$reference \\
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$input_reads \\
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> ${prefix}.paf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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minimap2: \$(minimap2 --version 2>&1)
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END_VERSIONS
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"""
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}
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