name: "ultra_index"
description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment
keywords:
  - uLTRA
  - index
  - minimap2
  - long_read
  - isoseq
  - ont
tools:
  - "ultra":
      description: "Splice aligner of long transcriptomic reads to genome."
      homepage: "https://github.com/ksahlin/uLTRA"
      documentation: "https://github.com/ksahlin/uLTRA"
      tool_dev_url: "https://github.com/ksahlin/uLTRA"
      doi: "10.1093/bioinformatics/btab540"
      licence: "['GNU GPLV3']"

input:
  - fasta:
      type: file
      description: A fasta file of the genome to use as reference for mapping
      pattern: "*.{fasta, fa}"
  - gtf:
      type: file
      description: An annotation file of the reference genome in GTF format
      pattern: "*.gtf"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - pickle:
      type: file
      description: Index files generated by uLTRA index
      pattern: "*.pickle"
  - pickle:
      type: file
      description: database file generated by uLTRA index
      pattern: "*.db"

authors:
  - "@sguizard"