name: "scramble_clusteridentifier"
description: The cluster_identifier tool of Scramble identifies soft clipped clusters
keywords:
  - bam
  - cram
  - soft-clipped clusters
tools:
  - "scramble":
      description: "Soft Clipped Read Alignment Mapper"
      homepage: "https://github.com/GeneDx/scramble"
      documentation: "https://github.com/GeneDx/scramble"
      tool_dev_url: "https://github.com/GeneDx/scramble"
      doi: ""
      licence: "['CC']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"
  - input_index:
      type: file
      description: Index of the BAM/CRAM file
      pattern: "*.{bai,crai}"
  - fasta:
      type: file
      description: The reference FASTA file (mandatory when using CRAM files)
      pattern: "*.{fasta,fa}"

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"
  - clusters:
      type: file
      description: Tab-delimited file containing the soft-clipped clusters
      pattern: "*.clusters.txt"

authors:
  - "@nvnieuwk"