name: bamaligncleaner
description: removes unused references from header of sorted BAM/CRAM files.
keywords:
  - bam
tools:
  - bamaligncleaner:
      description: Removes unaligned references in aligned BAM alignment file
      homepage: https://github.com/maxibor/bamAlignCleaner
      documentation: https://github.com/maxibor/bamAlignCleaner
      tool_dev_url: https://github.com/maxibor/bamAlignCleaner
      licence: ['GPL v3']

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 ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bam:
      type: file
      description: Sorted BAM/CRAM file
      pattern: "*.{bam,cram}"

authors:
  - "@jfy133"