mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 13:23:09 +00:00
9fb26ae462
* Add IDR module * Add meta and implement main todos * Modifying idr tests * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update main.nf * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test with new file name Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
56 lines
1.9 KiB
Text
56 lines
1.9 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process IDR {
|
|
tag "$prefix"
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5"
|
|
} else {
|
|
container "quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5"
|
|
}
|
|
|
|
input:
|
|
path peaks
|
|
val peak_type
|
|
val prefix
|
|
|
|
output:
|
|
path "*idrValues.txt", emit: idr
|
|
path "*log.txt" , emit: log
|
|
path "*.png" , emit: png
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
if (peaks.toList().size < 2) {
|
|
log.error "[ERROR] idr needs at least two replicates only one provided."
|
|
}
|
|
def peak_types = ['narrowPeak', 'broadPeak', 'bed']
|
|
if (!peak_types.contains(peak_type)) {
|
|
log.error "[ERROR] Invalid option: '${peak_type}'. Valid options for 'peak_type': ${peak_types.join(', ')}."
|
|
}
|
|
def idr_vals = prefix ? "${prefix}.idrValues.txt" : "idrValues.txt"
|
|
def log_file = prefix ? "${prefix}.log.txt" : "log.txt"
|
|
"""
|
|
idr \\
|
|
--samples $peaks \\
|
|
--input-file-type $peak_type \\
|
|
--output-file $idr_vals \\
|
|
--log-output-file $log_file \\
|
|
--plot \\
|
|
$options.args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|