mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
40 lines
1.4 KiB
Text
40 lines
1.4 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
process RSEQC_READDUPLICATION {
|
||
|
|
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/rseqc:3.0.1--py37h516909a_1"
|
||
|
|
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
|
||
|
|
|
||
|
|
conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(bam)
|
||
|
|
val options
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls
|
||
|
|
tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls
|
||
|
|
tuple val(meta), path("*.pdf") , emit: pdf
|
||
|
|
tuple val(meta), path("*.r") , emit: rscript
|
||
|
|
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}"
|
||
|
|
"""
|
||
|
|
read_duplication.py \\
|
||
|
|
-i $bam \\
|
||
|
|
-o $prefix \\
|
||
|
|
$ioptions.args
|
||
|
|
|
||
|
|
read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|