mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
c485109d9b
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bamAlignCleaner module * Add container tags * Update modules/bamaligncleaner/main.nf
40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BAMALIGNCLEANER {
|
|
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::bamaligncleaner=0.2.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0"
|
|
} else {
|
|
container "quay.io/biocontainers/bamaligncleaner:0.2.1--pyhdfd78af_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam"), emit: bam
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
|
|
"""
|
|
bamAlignCleaner \\
|
|
$options.args \\
|
|
-o ${prefix}.bam \\
|
|
${bam}
|
|
|
|
echo \$(bamAlignCleaner --version) | sed 's/.*version //' > ${software}.version.txt
|
|
"""
|
|
}
|