name: ultra_pipeline
description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection
keywords:
  - uLTRA
  - minimap2
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: "*.{fasta,fastq}"
  - genome:
      type: file
      description: fasta file of reference genome
      pattern: "*.fasta"
  - gtf:
      type: file
      description: A annotation of use the genome
      pattern: "*.gtf"

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

authors:
  - "@sguizard"
  - "@lassefolkersen"
  - "@ksahlin"