mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
b552958341
* add paraclu * remove TODOs * add min_cluster as input parameter, remove option parameters * add tool_dev_url
45 lines
1.6 KiB
Text
45 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PARACLU {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::paraclu=10" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1"
|
|
} else {
|
|
container "quay.io/biocontainers/paraclu:10--h9a82719_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bed)
|
|
val(min_cluster)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bed"), emit: bed
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def VERSION=10
|
|
"""
|
|
|
|
awk -F "\t" '{print\$1"\t"\$6"\t"\$2"\t"\$5}' < $bed > ${bed}_4P
|
|
sort -k1,1 -k3n ${bed}_4P > ${bed}_4Ps
|
|
paraclu $min_cluster ${bed}_4Ps > ${prefix}.clustered
|
|
paraclu-cut ${prefix}.clustered > ${prefix}.clustered.simplified
|
|
awk -F '\t' '{print \$1"\t"\$3"\t"\$4"\t"\$1":"\$3".."\$4","\$2"\t"\$6"\t"\$2}' ${prefix}.clustered.simplified > ${prefix}.clustered.simplified.bed
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|