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
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"
