name: bcftools_mpileup
description: Compresses VCF files
keywords:
    - variant calling
    - mpileup
    - VCF
tools:
    - mpileup:
        description: |
          Generates genotype likelihoods at each genomic position with coverage.
        homepage: http://samtools.github.io/bcftools/bcftools.html
        documentation: http://www.htslib.org/doc/bcftools.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: Input BAM file
        pattern: "*.{bam}"
    - fasta:
        type: file
        description: FASTA reference file
        pattern: "*.{fasta,fa}"
output:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - vcf:
        type: file
        description: VCF gzipped output file
        pattern: "*.{vcf.gz}"
    - tbi:
        type: file
        description: tabix index file
        pattern: "*.{tbi}"
    - stats:
        type: file
        description: Text output file containing stats
        pattern: "*{stats.txt}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@joseespinosa"
    - "@drpatelh"
