name: leehom
description: Bayesian reconstruction of ancient DNA fragments
keywords:
  - ancient DNA
  - adapter removal
  - clipping
  - trimming
  - merging
  - collapsing
  - preprocessing
  - bayesian
tools:
  - leehom:
      description: Bayesian reconstruction of ancient DNA fragments
      homepage: "https://grenaud.github.io/leeHom/"
      documentation: "https://github.com/grenaud/leeHom"
      tool_dev_url: "https://github.com/grenaud/leeHom"
      doi: "10.1093/nar/gku699"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: Unaligned BAM or one or two gzipped FASTQ file(s)
      pattern: "*.{bam,fq.gz,fastq.gz}"

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: BAM file
      pattern: "*.bam"
  - fq_pass:
      type: file
      description: Trimmed and merged FASTQ
      pattern: "*.fq.gz"
  - fq_fail:
      type: file
      description: Failed trimmed and merged FASTQs
      pattern: "*.fail.fq.gz"
  - unmerged_r1_fq_pass:
      type: file
      description: Passed unmerged R1 FASTQs
      pattern: "*.r1.fq.gz"
  - unmerged_r1_fq_fail:
      type: file
      description: Failed unmerged R1 FASTQs
      pattern: "*.r1.fail.fq.gz"
  - unmerged_r2_fq_pass:
      type: file
      description: Passed unmerged R2 FASTQs
      pattern: "*.r2.fq.gz"
  - unmerged_r2_fq_pass:
      type: file
      description: Failed unmerged R2 FASTQs
      pattern: "*.r2.fail.fq.gz"
  - log:
      type: file
      description: Log file of command
      pattern: "*.log"

authors:
  - "@jfy133"