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35 lines
934 B
Plaintext
35 lines
934 B
Plaintext
process MINIMAP2_INDEX {
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label 'process_medium'
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// Note: the versions here need to match the versions used in minimap2/align
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conda "bioconda::minimap2=2.24"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/minimap2:2.24--h7132678_1' :
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'quay.io/biocontainers/minimap2:2.24--h7132678_1' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*.mmi"), emit: index
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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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minimap2 \\
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-t $task.cpus \\
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-d ${fasta.baseName}.mmi \\
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$args \\
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$fasta
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cat <<-END_VERSIONS > versions.yml
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"${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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