name: samtools_stats
description: Produces comprehensive statistics from SAM/BAM/CRAM file
keywords:
    - statistics
    - 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
params:
    - outdir:
        type: string
        description: |
            The pipeline's output directory. By default, the module will
            output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
        type: string
        description: |
            Value for the Nextflow `publishDir` mode parameter.
            Available: symlink, rellink, link, copy, copyNoFollow, move.
    - enable_conda:
        type: boolean
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
    - singularity_pull_docker_container:
        type: boolean
        description: |
            Instead of directly downloading Singularity images for use with Singularity,
            force the workflow to pull and convert Docker containers instead.
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 ]
    - stats:
        type: file
        description: File containing samtools stats output
        pattern: "*.{stats}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@drpatelh"