mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
71 lines
3 KiB
Text
71 lines
3 KiB
Text
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
|
|
"""
|
|
}
|