name: tiddit_sv
description: Identify chromosomal rearrangements.
keywords:
  - structural
  - variants
  - vcf
tools:
  - sv:
      description: Search for structural variants.
      homepage: https://github.com/SciLifeLab/TIDDIT
      documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md
      doi: 10.12688/f1000research.11168.1
      licence: ["GPL-3.0-or-later"]
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: BAM/CRAM index file
      pattern: "*.{bai,crai}"
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test_fasta']`
  - fasta:
      type: file
      description: Input FASTA file
      pattern: "*.{fasta,fa}"
  - meta3:
      type: map
      description: |
        Groovy Map containing sample information from bwa index
        e.g. `[ id:'test_bwa-index' ]`
  - bwa_index:
      type: file
      description: BWA genome index files
      pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: vcf
      pattern: "*.{vcf}"
  - ploidy:
      type: file
      description: tab
      pattern: "*.{ploidies.tab}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@maxulysse"
maintainers:
  - "@maxulysse"
