{% set name = "umicollapse" %}
{% set version = "1.1.0" %}
{% set sha256 = "01b8ff5b6bcc775b277e92f5414e7e94019bfbe47fe0850810ab4e33500992b1"%}

package:
  name: {{ name }}
  version: {{ version }}

build:
  number: 0
  noarch: generic
  run_exports:
    - {{ pin_subpackage(name, max_pin="x") }}

source:
  url: https://github.com/siddharthab/UMICollapse/archive/refs/tags/v{{ version }}.tar.gz
  sha256: {{ sha256 }}

requirements:
  run:
    - openjdk >=17
    - python

test:
  commands:
    - which umicollapse

about:
  home: https://github.com/Daniel-Liu-c0deb0t/UMICollapse
  license: MIT
  license_family: MIT
  summary: Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI).
  description:
    UMIs are a popular way to identify duplicate DNA/RNA reads caused by PCR amplification. This requires software for 
    collapsing duplicate reads with the same UMI, while accounting for sequencing/PCR errors. This tool implements many 
    efficient algorithms for orders-of-magnitude faster UMI deduplication than previous tools (UMI-tools, etc.), 
    while maintaining similar functionality. This is achieved by using faster data structures with n-grams and BK-trees, 
    along other techniques that are carefully implemented to scale well to larger datasets and longer UMIs. Users of 
    UMICollapse have reported speedups from taking hours or days to run with a previous tool to taking only a few 
    minutes with this tool with real datasets! doi 10.7717/peerj.8275.
