nf-core_modules/modules/phantompeakqualtools/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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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:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
} else {
container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
}
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input:
tuple val(meta), path(bam)
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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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
RUN_SPP=`which run_spp.R`
Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
echo $VERSION > ${software}.version.txt
"""
}