name: samblaster
description: |
  This module combines samtools and samblaster in order to use
  samblaster capability to filter or tag SAM files, with the advantage
  of maintaining both input and output in BAM format.
  Samblaster input must contain a sequence header: for this reason it has been piped
  with the "samtools view -h" command.
  Additional desired arguments for samtools can be passed using:
  options.args2 for the input bam file
  options.args3 for the output bam file
keywords:
  - sort
tools:
  - samblaster:
      description: |
        samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.
        It can also optionally output discordant read pairs and/or split read mappings to separate SAM files,
        and/or unmapped/clipped reads to a separate FASTQ file.
        By default, samblaster reads SAM input from stdin and writes SAM to stdout.
      homepage: None
      documentation: https://github.com/GregoryFaust/samblaster
      tool_dev_url: https://github.com/GregoryFaust/samblaster
      doi: "10.1093/bioinformatics/btu314"
      licence: ["MIT"]

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

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: Tagged or filtered BAM file
      pattern: "*.bam"

authors:
  - "@lescai"