name: gstama_polyacleanup
description: Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)
keywords:
  - gstama
  - gstama/polyacleanup
  - long-read
  - isoseq
  - 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 ]
  - fasta:
      type: file
      description: Full Length Non Chimeric reads in fasta format
      pattern: "*.{fa,fasta}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - fasta:
      type: file
      description: The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip.
      pattern: "*_tama.fa.gz"
  - report:
      type: file
      description: A text file describing the number of polyA tails removed and their length. Compressed with gzip.
      pattern: "*_tama_polya_flnc_report.txt.gz"
  - tails:
      type: file
      description: A gzip compressed FASTA file of trimmed polyA tails.
      pattern: "*_tama_tails.fa.gz"

authors:
  - "@sguizard"