nf-core_modules/modules/idr/main.nf
2022-02-04 09:53:32 +01:00

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process IDR {
tag "$prefix"
label 'process_low'
conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' :
'quay.io/biocontainers/idr:2.0.4.2--py39hcbe4a3b_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
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
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 \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
idr: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//')
END_VERSIONS
"""
}