mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
50 lines
1.7 KiB
Text
50 lines
1.7 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process IVAR_VARIANTS {
|
|
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), 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 fasta
|
|
path gff
|
|
|
|
output:
|
|
tuple val(meta), path("*.tsv") , emit: tsv
|
|
tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
|
|
def features = params.gff ? "-g $gff" : ""
|
|
"""
|
|
samtools mpileup \\
|
|
$options.args2 \\
|
|
--reference $fasta \\
|
|
$bam | \\
|
|
$save_mpileup \\
|
|
ivar variants \\
|
|
$options.args \\
|
|
$features \\
|
|
-r $fasta \\
|
|
-p $prefix
|
|
|
|
echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|