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

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - 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"
  - css:
      type: file
      description: Consensus sequences
      pattern: "*.ccs.bam"

authors:
  - "@sguizard"