mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
dce27b8102
* Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process IVAR_CONSENSUS {
|
|
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::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
|
|
|
|
output:
|
|
tuple val(meta), path("*.fa") , emit: fasta
|
|
tuple val(meta), path("*.qual.txt"), emit: qual
|
|
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 |" : ""
|
|
"""
|
|
samtools mpileup \\
|
|
--reference $fasta \\
|
|
$options.args2 \\
|
|
$bam | \\
|
|
$save_mpileup \\
|
|
ivar consensus \\
|
|
$options.args \\
|
|
-p $prefix
|
|
|
|
echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|