nf-core_modules/software/artic/minion/main.nf

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// 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
"""
}