mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
7be60774b6
* add module for tbprofiler * Update test.yml * Update meta.yml Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
48 lines
1.8 KiB
Text
48 lines
1.8 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process TBPROFILER_PROFILE {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${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::tb-profiler=3.0.8" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0"
|
|
} else {
|
|
container "quay.io/biocontainers/tb-profiler:3.0.8--pypyh5e36f6f_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
|
|
output:
|
|
tuple val(meta), path("bam/*.bam") , emit: bam
|
|
tuple val(meta), path("results/*.csv") , emit: csv, optional: true
|
|
tuple val(meta), path("results/*.json"), emit: json
|
|
tuple val(meta), path("results/*.txt") , emit: txt, optional: true
|
|
tuple val(meta), path("vcf/*.vcf.gz") , emit: vcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def input_reads = meta.single_end ? "--read1 $reads" : "--read1 ${reads[0]} --read2 ${reads[1]}"
|
|
"""
|
|
tb-profiler \\
|
|
profile \\
|
|
$options.args \\
|
|
--prefix ${prefix} \\
|
|
--threads $task.cpus \\
|
|
$input_reads
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$( echo \$(tb-profiler --version 2>&1) | sed 's/TBProfiler version //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|