name: rseqc_tin
description: Calculte TIN (transcript integrity number) from RNA-seq reads
keywords:
  - rnaseq
  - transcript
  - integrity
tools:
  - rseqc:
      description: |
        RSeQC package provides a number of useful modules that can comprehensively evaluate
        high throughput sequence data especially RNA-seq data.
      homepage: http://rseqc.sourceforge.net/
      documentation: http://rseqc.sourceforge.net/
      doi: 10.1093/bioinformatics/bts356
      licence: ['GPL-3.0-or-later']
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Input BAM file
      pattern: "*.{bam}"
  - bai:
    type: file
    description: Index for input BAM file
    pattern: "*.{bai}"
  - bed:
      type: file
      description: BED file containing the reference gene model
      pattern: "*.{bed}"
output:
  - txt:
      type: file
      description: TXT file containing tin.py results summary
      pattern: "*.txt"
  - xls:
      type: file
      description: XLS file containing tin.py results
      pattern: "*.xls"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"