mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
def options = initOptions(params.options)
|
||
|
|
|
||
|
|
process IVAR_TRIM {
|
||
|
|
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), publish_id:meta.id) }
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(bam)
|
||
|
|
path bed
|
||
|
|
|
||
|
|
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}"
|
||
|
|
"""
|
||
|
|
ivar trim \\
|
||
|
|
$options.args \\
|
||
|
|
-i $bam \\
|
||
|
|
-b $bed \\
|
||
|
|
-p $prefix
|
||
|
|
|
||
|
|
ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|