name: variantbam
description: Filtering, downsampling and profiling alignments in BAM/CRAM formats
keywords:
  - filter
  - bam
  - subsample
  - downsample
  - downsample bam
  - subsample bam
tools:
  - variantbam:
      description: Filtering and profiling of next-generational sequencing data using region-specific rules
      homepage: https://github.com/walaj/VariantBam
      documentation: https://github.com/walaj/VariantBam#table-of-contents
      tool_dev_url: https://github.com/walaj/VariantBam
      doi: 10.1093/bioinformatics/btw111
      licence: ['Apache2']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - bam:
      type: file
      description: Filtered or downsampled BAM file
      pattern: "*.{bam}"

authors:
  - "@bjohnnyd"