name: samtools_flagstat
description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
keywords:
    - stats
    - mapping
    - counts
    - bam
    - sam
    - cram
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: hhttp://www.htslib.org/doc/samtools.html
        doi: 10.1093/bioinformatics/btp352
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
        pattern: "*.{bam,cram,sam}"
    - bai:
        type: file
        description: Index for BAM/CRAM/SAM file
        pattern: "*.{bai,crai,sai}"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - flagstat:
        type: file
        description: File containing samtools flagstat output
        pattern: "*.{flagstat}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@drpatelh"
