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 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 """ }