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43 lines
1.5 KiB
Text
43 lines
1.5 KiB
Text
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process GENOMESCOPE2 {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5':
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'quay.io/biocontainers/genomescope2:2.0--py310r41hdfd78af_5' }"
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input:
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tuple val(meta), path(histogram)
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output:
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tuple val(meta), path("$prefix-linear_plot.png") , emit: linear_plot_png
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tuple val(meta), path("$prefix-transformed_linear_plot.png"), emit: transformed_linear_plot_png
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tuple val(meta), path("$prefix-log_plot.png") , emit: log_plot_png
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tuple val(meta), path("$prefix-transformed_log_plot.png") , emit: transformed_log_plot_png
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tuple val(meta), path("$prefix-model.txt") , emit: model
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tuple val(meta), path("$prefix-summary.txt") , emit: summary
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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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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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genomescope2 \\
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--input $histogram \\
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$args \\
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--output . \\
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--name_prefix $prefix
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ls -l
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cat <<-END_VERSIONS > versions.yml
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'${task.process}':
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genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' )
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END_VERSIONS
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"""
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}
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