name: "scramble_clusteranalysis"
description: The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by `cluster_identifier`
keywords:
  - soft-clipped clusters
  - scramble
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 ]
  - clusters:
      type: file
      description: Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier
      pattern: "*clusters.txt"
  - fasta:
      type: file
      description: Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions.
      pattern: "*.{fasta,fa}"
  - mei_ref:
      type: file
      description: Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct
      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"
  - meis_tab:
      type: file
      description: Tab-delimited text file containing MEI calls
      pattern: "*_MEIs.txt"
  - dels_tab:
      type: file
      description: Tab-delimited text file containing predicted deletions
      pattern: "*_PredictedDeletions.txt"
  - vcf:
      type: file
      description: A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)
      pattern: "*.vcf"

authors:
  - "@nvnieuwk"