---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "eklipse"
description: tool for detection and quantification of large mtDNA rearrangements.
keywords:
  - eklipse
  - mitochondria
  - mtDNA
  - circos
  - deletion
  - SV
tools:
  - "eklipse":
      description: "tool for detection and quantification of large mtDNA rearrangements."
      homepage: "https://github.com/dooguypapua/eKLIPse/tree/master"
      documentation: "https://github.com/dooguypapua/eKLIPse/tree/master"
      tool_dev_url: "https://github.com/dooguypapua/eKLIPse/tree/master"
      doi: "10.1038/s41436-018-0350-8"
      licence: ["GNU General Public v3 or later (GPL v3+)"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: MT BAM/SAM file
      pattern: "*.{bam,sam}"
  - bai:
      type: file
      description: MT BAM/SAM index file
      pattern: "*.{bai,sai}"
  - ref_gb:
      type: file
      description: mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb will be used
      pattern: "*.{gb}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - csv:
      type: file
      description: csv file containing deletions
      pattern: "*.{csv}"
  - circos:
      type: file
      description: png file with circos plot of mt
      pattern: "*.{png}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@Lucpen"
