2020-09-10 15:45:11 +00:00
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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def VERSION = '1.2.2'
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process PHANTOMPEAKQUALTOOLS {
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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:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
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//container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
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conda (params.conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
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input:
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tuple val(meta), path(bam)
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val options
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output:
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tuple val(meta), path("*.out") , emit: spp
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tuple val(meta), path("*.pdf") , emit: pdf
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tuple val(meta), path("*.Rdata"), emit: rdata
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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"""
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RUN_SPP=`which run_spp.R`
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Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
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echo $VERSION > ${software}.version.txt
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"""
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}
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