nf-core_modules/modules/samtools/stats/meta.yml

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
        licence: ['MIT']
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - input:
      type: file
      description: BAM/CRAM file from alignment
      pattern: "*.{bam,cram}"
    - input_index:
      type: file
      description: BAI/CRAI file from alignment
      pattern: "*.{bai,crai}"
    - fasta:
        type: optional file
        description: Reference file the CRAM was created with
        pattern: "*.{fasta,fa}"
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}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@drpatelh"
    - "@FriederikeHanssen"