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61c88c6233
* fix: remove left-over unnecessary code * Add hamronizer/deeparg * Add hamronisation/summarise * Update test.yml * Update modules/hamronization/summarize/meta.yml Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * line up outputs Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
process HAMRONIZATION_SUMMARIZE {
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
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'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
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input:
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path(reports)
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val(format)
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output:
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path("hamronization_combined_report.json"), optional: true, emit: json
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path("hamronization_combined_report.tsv") , optional: true, emit: tsv
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path("hamronization_combined_report.html"), optional: true, emit: html
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def outformat = format == 'interactive' ? 'html' : format
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"""
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hamronize \\
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summarize \\
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${reports.join(' ')} \\
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-t ${format} \\
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$args \\
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-o hamronization_combined_report.${outformat}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
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END_VERSIONS
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"""
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}
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