name: "retroseq_call"
description: RetroSeq is a tool for discovery and genotyping of transposable element variants (TEVs) from next-gen sequencing reads aligned to a reference genome in BAM format.
keywords:
  - retroseq
  - transposable elements
  - genomics
tools:
  - "retroseq":
      description: "RetroSeq: discovery and genotyping of TEVs from reads in BAM format."
      homepage: "https://github.com/tk2/RetroSeq"
      documentation: "https://github.com/tk2/RetroSeq"
      tool_dev_url: "https://github.com/tk2/RetroSeq"
      doi: "10.1093/bioinformatics/bts697"
      licence: "['GPL']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - tab:
      type: file
      description: Output file from running retroseq -call
      pattern: "*.tab"
  - bam:
      type: file
      description: Sorted BAM file
      pattern: "*.bam"
  - bai:
      type: file
      description: Index of the sorted BAM file
      pattern: "*.bam"
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - fasta:
      type: file
      description: Reference genome in fasta format
      pattern: "*.fasta"
  - meta3:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - fai:
      type: file
      description: Reference FASTA index
      pattern: "*.fai"

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"
  - vcf:
      type: file
      description: Output file containing TEVs and their location in the genome.
      pattern: "*.vcf"

authors:
  - "@peterpru"
