name: gstama_merge
description: Merge multiple transcriptomes while maintaining source information.
keywords:
  - gstama
  - gstama/merge
  - long-read
  - isoseq
  - nanopore
  - tama
  - trancriptome
  - annotation
tools:
  - gstama:
      description: Gene-Switch Transcriptome Annotation by Modular Algorithms
      homepage: https://github.com/sguizard/gs-tama
      documentation: https://github.com/GenomeRIK/tama/wiki
      tool_dev_url: https://github.com/sguizard/gs-tama
      doi: "https://doi.org/10.1186/s12864-020-07123-7"
      licence: ["GPL v3 License"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: bed12 file generated by TAMA collapse
      pattern: "*.bed"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - tsv:
      type: file
      description: A three columns TSV files listing annotations to merge. For each annotation, state if the mRNAs are capped and the priority of merging.
      pattern: "*.bed"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@sguizard"
