name: samtools sort
description: Sort a BAM or CRAM file
keywords:
    - sort
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:
    -
        - input:
            type: file
            description: Input BAM or CRAM file
            pattern: *.{bam,cram}
output:
    -
        - index:
            type: file
            description: BAM or CRAM index file
            pattern: *.{bai}
authors:
    - @ewels