name: samtools_fixmate
description: Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.
keywords:
    - fixmate
    - samtools
    - insert size
    - repair
    - bam
    - paired
    - read pairs
tools:
    - samtools:
        description: |
            SAMtools is a set of utilities for interacting with and post-processing
            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
            These files are generated as output by short read aligners like BWA.
        homepage: http://www.htslib.org/
        documentation: http://www.htslib.org/doc/samtools.html
        tool_dev_url: https://github.com/samtools/samtools
        doi: 10.1093/bioinformatics/btp352
        licence: ['MIT']
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/CRAM/SAM file, must be sorted by name, not coordinate
      pattern: "*.{bam,cram,sam}"

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/CRAM/SAM file with mate information added and/or proper pairs recalled
      pattern: "*.{bam,cram,sam}"

authors:
  - "@sppearce"