name: "atlas_splitmerge"
description: split single end read groups by length and merge paired end reads
keywords:
  - split
  - merge
  - bam
  - read group
tools:
  - "atlas":
      description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
      homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
      documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
      tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
      doi: "10.1101/105346"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - bam:
      type: file
      description: Single input BAM file.
      pattern: "*.bam"
  - bai:
      type: file
      description: The BAI file for the input BAM file
      pattern: "*.bai"
  - read_group_setting:
      type: file
      description: |
        TXT file containing the split and merge settings for
        each readgroup. Each line consist of one readgroup,
        single/double identifier and the maximum cycle number
        of the sequencer. e.g. "RG1 single 100"
      pattern: "*.txt"
  - blacklist:
      type: file
      description: |
        blacklist.txt (optional), A txt file with blacklisted read names
        that should be ignored and just written to file, each on a new line
      pattern: "*.txt"

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: A BAM file with suffix_mergedReads.bam
      pattern: "*_mergedReads.bam"

  - filelist:
      type: file
      description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz
      pattern: "*.txt.gz"

authors:
  - "@merszym"