nf-core_modules/software/phantompeakqualtools/main.nf
2020-08-05 17:16:34 +01:00

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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
"""
}