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42 lines
1.5 KiB
Text
42 lines
1.5 KiB
Text
process GENESCOPEFK {
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tag "$meta.id"
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label 'process_low'
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if (params.enable_conda) {
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error "Conda environments cannot be used when using the GeneScope tool. Please use docker or singularity containers."
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}
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container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
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input:
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tuple val(meta), path(fastk_histex_histogram)
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output:
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tuple val(meta), path("*_linear_plot.png") , emit: linear_plot
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tuple val(meta), path("*_log_plot.png") , emit: log_plot
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tuple val(meta), path("*_model.txt") , emit: model
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tuple val(meta), path("*_summary.txt") , emit: summary
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tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot
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tuple val(meta), path("*_transformed_log_plot.png") , emit: transformed_log_plot
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def GENESCOPE_VERSION = '380815c420f50171f9234a0fd1ff426b39829b91' // Git commit id is used instead of GeneScopeFK.R -v as software is not release versioned.
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"""
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GeneScopeFK.R \\
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$args \\
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--input $fastk_histex_histogram \\
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--output . \\
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--name_prefix ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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genescope: $GENESCOPE_VERSION
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r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
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END_VERSIONS
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"""
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}
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