mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
f8ea9828cd
* Add artic minion module * Add fast5 to test data configuration * Add test for artic minion
73 lines
3.2 KiB
Text
73 lines
3.2 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process ARTIC_MINION {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
publishDir "${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::artic=1.2.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
|
|
} else {
|
|
container "quay.io/biocontainers/artic:1.2.1--py_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(fastq)
|
|
path fast5_dir
|
|
path sequencing_summary
|
|
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
|
|
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
|
|
path medaka_model
|
|
val scheme
|
|
val scheme_version
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}.*") , emit: results
|
|
tuple val(meta), path("${prefix}.sorted.bam") , emit: bam
|
|
tuple val(meta), path("${prefix}.sorted.bam.bai") , emit: bai
|
|
tuple val(meta), path("${prefix}.trimmed.rg.sorted.bam") , emit: bam_trimmed
|
|
tuple val(meta), path("${prefix}.trimmed.rg.sorted.bam.bai") , emit: bai_trimmed
|
|
tuple val(meta), path("${prefix}.primertrimmed.rg.sorted.bam") , emit: bam_primertrimmed
|
|
tuple val(meta), path("${prefix}.primertrimmed.rg.sorted.bam.bai"), emit: bai_primertrimmed
|
|
tuple val(meta), path("${prefix}.consensus.fasta") , emit: fasta
|
|
tuple val(meta), path("${prefix}.pass.vcf.gz") , emit: vcf
|
|
tuple val(meta), path("${prefix}.pass.vcf.gz.tbi") , emit: tbi
|
|
tuple val(meta), path("*.json"), optional:true , emit: json
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def version = scheme_version.toString().toLowerCase().replaceAll('v','')
|
|
def fast5 = params.fast5_dir ? "--fast5-directory $fast5_dir" : ""
|
|
def summary = params.sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
|
|
def model = ""
|
|
if (options.args.tokenize().contains('--medaka')) {
|
|
fast5 = ""
|
|
summary = ""
|
|
model = file(params.artic_minion_medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $params.artic_minion_medaka_model"
|
|
}
|
|
"""
|
|
artic \\
|
|
minion \\
|
|
$options.args \\
|
|
--threads $task.cpus \\
|
|
--read-file $fastq \\
|
|
--scheme-directory ./primer-schemes \\
|
|
--scheme-version $version \\
|
|
$model \\
|
|
$fast5 \\
|
|
$summary \\
|
|
$scheme \\
|
|
$prefix
|
|
|
|
echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|