mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
51 lines
1.8 KiB
Text
51 lines
1.8 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process MACS2_CALLPEAK {
|
|
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), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1"
|
|
} else {
|
|
container "quay.io/biocontainers/macs2:2.2.7.1--py38h0213d0e_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(ipbam), path(controlbam)
|
|
val macs2_gsize
|
|
|
|
output:
|
|
tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
|
|
tuple val(meta), path("*.xls") , emit: xls
|
|
path "*.version.txt" , emit: version
|
|
|
|
tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
|
|
tuple val(meta), path("*.bed") , optional:true, emit: bed
|
|
tuple val(meta), path("*.bdg") , optional:true, emit: bdg
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def format = meta.single_end ? 'BAM' : 'BAMPE'
|
|
def control = controlbam ? "--control $controlbam" : ''
|
|
"""
|
|
macs2 \\
|
|
callpeak \\
|
|
$options.args \\
|
|
--gsize $macs2_gsize \\
|
|
--format $format \\
|
|
--name $prefix \\
|
|
--treatment $ipbam \\
|
|
$control
|
|
|
|
macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
|
|
"""
|
|
}
|