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38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process APPYTER {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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// FIXME These rely on docker and won't work with conda
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// conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "$options.appyter_image"
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} else {
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container "$options.appyter_image}"
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}
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input:
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path input
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output:
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path "data/output.ipynb", emit: output_notebook
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path "*.version.txt" , emit: version
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script:
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// Add soft-links to original FastQs for consistent naming in pipeline
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
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"""
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appyter nbconstruct -i $input -o data/output.ipynb
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"""
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}
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