Add phantompeakqualtools

software/phantompeakqualtools/functions.nf

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+../lib/functions.nf

software/phantompeakqualtools/main.nf

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