name: stringtie_merge
description: Merges the annotation gtf file and the stringtie output gtf files
keywords:
  - merge
  - gtf
  - reference
tools:
  - stringtie2:
      description: |
        Transcript assembly and quantification for RNA-Seq
      homepage: https://ccb.jhu.edu/software/stringtie/index.shtml
      documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
      licence: ["MIT"]
input:
  - stringtie_gtf:
      type: file
      description: |
        Stringtie transcript gtf output(s).
      pattern: "*.gtf"
  - annotation_gtf:
      type: file
      description: |
        Annotation gtf file (optional).
      pattern: "*.gtf"
output:
  - merged_gtf:
      type: map
      description: |
        Merged gtf from annotation and stringtie output gtfs.
      pattern: "*.gtf"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@yuukiiwa"
