name: "MINDAGAP_DUPLICATEFINDER"
description: marks duplicate spots along gridline edges.
keywords:
  - imaging
  - resolve_bioscience
  - spatial_transcriptomics
tools:
  - "mindagap":
      description: "Takes a single panorama image and fills the empty grid lines with neighbour-weighted values."
      homepage: "https://github.com/ViriatoII/MindaGap/blob/main/README.md"
      documentation: "https://github.com/ViriatoII/MindaGap/blob/main/README.md"
      tool_dev_url: "https://github.com/ViriatoII/MindaGap"
      licence: ["BSD 3-clause License"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - spot_table:
      type: file
      description: tsv file containing one spot per row with order x,y,z,gene without column header.
      pattern: "*.{tsv,txt}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - marked_dups_spots:
      type: file
      description: tsv file containing one spot per row, with duplicated spots labeled with "Duplicated" in their gene column.
      pattern: "*.{markedDups.txt}"

authors:
  - "@FloWuenne"
maintainers:
  - "@FloWuenne"
