name: lima
description: lima - The PacBio Barcode Demultiplexer and Primer Remover
keywords:
  - sort
tools:
  - lima:
      description: lima - The PacBio Barcode Demultiplexer and Primer Remover
      homepage: https://github.com/PacificBiosciences/pbbioconda
      documentation: https://lima.how/
      tool_dev_url: https://github.com/pacificbiosciences/barcoding/
      doi: ""
      licence: ['BSD-3-clause-Clear']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - ccs:
      type: file
      description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs
      pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}"
  - primers:
      type: file
      description: Fasta file, sequences of primers
      pattern: "*.fasta"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bam:
      type: file
      description: A bam file of ccs purged of primers
      pattern: "*.bam"
  - pbi:
      type: file
      description: Pacbio index file of ccs purged of primers
      pattern: "*.bam"
  - xml:
      type: file
      description: An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.
      pattern: "*.xml"
  - json:
      type: file
      description: A metadata json file
      pattern: "*.json"
  - clips:
      type: file
      description: A fasta file of clipped primers
      pattern: "*.clips"
  - counts:
      type: file
      description: A tabulated file of describing pairs of primers
      pattern: "*.counts"
  - guess:
      type: file
      description: A second tabulated file of describing pairs of primers (no doc available)
      pattern: "*.guess"
  - report:
      type: file
      description: A tab-separated file about each ZMW, unfiltered
      pattern: "*.report"
  - summary:
      type: file
      description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.
      pattern: "*.summary"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"

authors:
  - "@sguizard"