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
      licence: ["MIT"]
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}"
  - intervals:
      type: file
      description: Input intervals file. A file (commonly '.bed') containing regions to subset
  - meta:
      type: map
      description: |
        Groovy Map containing information about the genome fasta, e.g. [ id: 'sarscov2' ]
  - fasta:
      type: file
      description: FASTA reference file
      pattern: "*.{fasta,fa}"
  - save_mpileup:
      type: boolean
      description: Save mpileup file generated by bcftools mpileup
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: "*.{vcf.gz.tbi}"
  - stats:
      type: file
      description: Text output file containing stats
      pattern: "*{stats.txt}"
  - mpileup:
      type: file
      description: mpileup gzipped output for all positions
      pattern: "{*.mpileup.gz}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"
maintainers:
  - "@joseespinosa"
  - "@drpatelh"
