name: "umitools_dedup"
namespace: "umitools"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/nf-core/umitools/dedup/main.nf, modules/nf-core/umitools/dedup/meta.yml]
    last_sha: 54721c6946daf6d602d7069dc127deef9cbe6b33
description: |
  Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

argument_groups:
- name: "Input"
  arguments:   
  - name: "--paired"
    type: boolean 
    default: false
    description: Paired fastq files or not?
  - name: "--bam"
    type: file
    description: Input BAM file
  - name: "--bai"
    type: file
    description: BAM index
  - name: "--get_output_stats"
    type: boolean
    description: Whether or not to generate output stats.
    
- name: "Output"
  arguments:   
  - name: "--output_bam"
    type: file
    description: Deduplicated BAM file
    direction: output
    default: $id.$key.bam
  - name: "--output_stats"
    type: file
    description: Directory containing UMI based dedupllication statistics files
    direction: output
    default: $id.umi_dedup.stats

resources:
  - type: bash_script
    path: script.sh

test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/unit_test_resources/chr19.bam
  - path: /testData/unit_test_resources/chr19.bam.bai

engines:
- type: docker
  image: ubuntu:22.04
  setup:
    - type: apt
      packages: [pip]
    - type: python
      packages: [umi_tools]
runners: 
- type: executable
- type: nextflow