name: stringtie
description: Transcript assembly and quantification for RNA-Se
keywords:
  - transcript
  - assembly
  - quantification
  - gtf

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:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: |
        Stringtie transcript gtf output(s).
  - gtf:
      type: file
      description: |
        Annotation gtf file.
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - transcript_gtf:
      type: file
      description: transcript gtf
      pattern: "*.{transcripts.gtf}"
  - coverage_gtf:
      type: file
      description: coverage gtf
      pattern: "*.{coverage.gtf}"
  - abudance:
      type: file
      description: abudance
      pattern: "*.{abudance.txt}"
  - ballgown:
      type: file
      description: for running ballgown
      pattern: "*.{ballgown}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
