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7560689375
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
35 lines
1 KiB
Text
35 lines
1 KiB
Text
process SOURMASH_SKETCH {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0':
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'quay.io/biocontainers/sourmash:4.2.4--hdfd78af_0' }"
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input:
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tuple val(meta), path(sequence)
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output:
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tuple val(meta), path("*.sig"), emit: signatures
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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 ?: "dna --param-string 'scaled=1000,k=31'"
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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sourmash sketch \\
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$args \\
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--merge '${prefix}' \\
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--output '${prefix}.sig' \\
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$sequence
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
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END_VERSIONS
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"""
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}
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