name: isoseq3_refine
description: Generate transcripts by clustering HiFi reads
keywords:
  - isoseq3
  - isoseq3/refine
tools:
  - isoseq3:
      description: IsoSeq3 - Scalable De Novo Isoform Discovery
      homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
      documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
      tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
      doi: ""
      licence: ["BSD-3-Clause-Clear"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test ]
  - bam:
      type: file
      description: BAM file, cleaned ccs generated by lima
      pattern: "*.bam"
  - primers:
      type: file
      description: fasta file of primers
      pattern: "*.fasta"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bam:
      type: file
      description: Set of complete reads (with polyA tail), where the polyA has been trimmed
      pattern: "*.bam"
  - pbi:
      type: file
      description: Pacbio index file from polyA trimmed reads
      pattern: "*.pbi"
  - consensusreadset:
      type: file
      description: Metadata about read library
      pattern: "*.xml"
  - summary:
      type: file
      description: json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads
      pattern: "*.json"
  - report:
      type: file
      description: Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)
      pattern: "*.csv"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@sguizard"