mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
options = initOptions(params.options)
|
||
|
|
|
||
|
|
process LAST_DOTPLOT {
|
||
|
|
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::last=1219" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/last:1219--h2e03b76_0"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(maf)
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.{png,gif}"), emit: plot
|
||
|
|
path "*.version.txt" , emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
def format = options.args2 ? options.args2 : "png"
|
||
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
|
"""
|
||
|
|
last-dotplot \\
|
||
|
|
$options.args \\
|
||
|
|
$maf \\
|
||
|
|
$prefix.$format
|
||
|
|
|
||
|
|
# last-dotplot has no --version option so let's use lastal from the same suite
|
||
|
|
lastal --version | sed 's/lastal //' > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|