nf-core_modules/modules/artic/minion/main.nf
2022-02-04 09:53:32 +01:00

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process ARTIC_MINION {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
'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 "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def version = scheme_version.toString().toLowerCase().replaceAll('v','')
def fast5 = fast5_dir ? "--fast5-directory $fast5_dir" : ""
def summary = sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
def model = ""
if (args.tokenize().contains('--medaka')) {
fast5 = ""
summary = ""
model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
}
def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
"""
$hd5_plugin_path
artic \\
minion \\
$args \\
--threads $task.cpus \\
--read-file $fastq \\
--scheme-directory ./primer-schemes \\
--scheme-version $version \\
$model \\
$fast5 \\
$summary \\
$scheme \\
$prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
artic: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
END_VERSIONS
"""
}