name: pbccs
description: Pacbio ccs - Generate Higly Accurate Single-Molecule Consensus Reads
keywords:
  - ccs
tools:
  - pbccs:
      description: pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
      homepage: https://github.com/PacificBiosciences/pbbioconda
      documentation: https://ccs.how/
      tool_dev_url: https://github.com/PacificBiosciences/ccs

      licence: ["BSD-3-Clause-Clear"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        id: id of the split file
  - bam:
      type: file
      description: Raw subreads bam
      pattern: "*.subreads.bam"
  - pbi:
      type: file
      description: Pacbio BAM Index
      pattern: "*.pbi"
  - chunk_num:
      type: integer
      description: BAM part to process
  - chunk_on:
      type: integer
      description: Total number of bam parts to process

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"
  - bam:
      type: file
      description: CCS sequences in bam format
      pattern: "*.bam"
  - pbi:
      type: file
      description: PacBio Index of CCS sequences
      pattern: "*.pbi"
  - report_txt:
      type: file
      description: Summary of CCS in txt format
      pattern: ".txt"
  - report_json:
      type: file
      description: Summary of CCS in txt json
      pattern: ".json"
  - metrics:
      type: file
      description: Metrics about zmws
      pattern: "*.json.gz"

authors:
  - "@sguizard"
