name: artic_minion
description: |
    Run the alignment/variant-call/consensus logic of the artic pipeline
keywords:
  - artic
  - aggregate
  - demultiplexed reads
tools:
  - artic:
      description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
      homepage: https://artic.readthedocs.io/en/latest/
      documentation: https://artic.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/artic-network/fieldbioinformatics
      doi: ""
      licence: ['MIT']
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastq:
      type: file
      description:  FastQ file containing reads
      pattern: "*.{fastq.gz}"
  - fast5_dir:
      type: directory
      description:  Directory containing MinION FAST5 files
      pattern: "*"
  - sequencing_summary:
      type: file
      description: Path to Guppy sequencing summary
      pattern: "*.{txt}"
  - primer_scheme_fasta:
      type: file
      description: |
        Sequence of the reference genome used in the scheme in FASTA format
      pattern: "*.{reference.fasta}"
  - primer_scheme_bed:
      type: file
      description: |
        bed files containing coordinates of each primer in the scheme,
        relative to the reference genome
      pattern: "*.{scheme.bed}"
  - medaka_model:
      type: file
      description: |
        Medaka model to use (if option --medaka is set)
      pattern: "*.*"
  - scheme:
      type: value
      description: Name of the primer scheme
  - scheme_version:
      type: value
      description: Version of the primer scheme
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - results:
      type:
      description: Aggregated FastQ files
      pattern: "*.fastq.gz"
  - bam:
      type: file
      description: BAM file
      pattern: "*.{sorted.bam}"
  - bai:
      type: file
      description: BAM index file
      pattern: "*.{sorted.bai}"
  - bam_trimmed:
      type: file
      description: BAM file with the primers left on
      pattern: "*.{trimmed.rg.sorted.bam}"
  - bai_trimmed:
      type: file
      description: BAM index file of bam_trimmed
      pattern: "*.{sorted.bai}"
  - bam_primertrimmed:
      type: file
      description: BAM containing reads after primer-binding site trimming
      pattern: "*.{trimmed.rg.sorted.bam}"
  - bai_primertrimmed:
      type: file
      description: BAM index file of bam_primertrimmed
      pattern: "*.{primertrimmed.rg.sorted.bam.bai}"
  - fasta:
      type: file
      description: FAST file with consensus sequence
      pattern: "*.{consensus.fasta}"
  - vcf:
      type: file
      description: VCF file containing detected variants passing quality filter
      pattern: "*.{pass.vcf.gz}"
  - tbi:
      type: file
      description: VCF index
      pattern: "*.{pass.vcf.gz.tbi}"
  - json:
      type: file
      description: JSON file for MultiQC
      pattern: "*.json"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@joseespinosa"
  - "@drpatelh"