name: "ultra_align"
description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome
keywords:
  - uLTRA
  - align
  - 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:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: A fasta or fastq file of reads to align
      pattern: "*.{fa,fasta,fastq}"
  - genome:
      type: file
      description: A fasta file of reference genome
      pattern: "*.{fa,fasta}"
  - pickle:
      type: file
      description: Pickle files generated by uLTRA index
      pattern: "*.pickle"
  - db:
      type: file
      description: Database generated by uLTRA index
      pattern: "*.db"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bam:
      type: file
      description: The aligned reads in bam format
      pattern: "*.bam"

authors:
  - "@sguizard"
