name: pbbam_pbmerge
description: The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
keywords:
  - pbbam
  - pbbam/pbmerge
tools:
  - pbbam:
      description: PacBio BAM C++ library
      homepage: https://github.com/PacificBiosciences/pbbioconda
      documentation: https://pbbam.readthedocs.io/en/latest/tools/pbmerge.html
      tool_dev_url: https://github.com/pacificbiosciences/pbbam/
      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: BAM files to merge
      pattern: "*.bam"

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: The merged bam file
      pattern: "*.bam"
  - pbi:
      type: file
      description: BAM Pacbio index file
      pattern: "*.bam.pbi"

authors:
  - "@sguizard"