name: "mindagap_mindagap"
description: Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.
keywords:
  - imaging
  - resolve_bioscience
  - spatial_transcriptomics
tools:
  - "mindagap":
      description: "Mindagap is a collection of tools to process multiplexed FISH data, such as produced by Resolve Biosciences Molecular Cartography."
      homepage: "https://github.com/ViriatoII/MindaGap"
      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', single_end:false ]
  - panorama:
      type: file
      description: A tiff file containing gridlines as produced by Molecular Cartography imaging.
      pattern: "*.{tif,tiff}"
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"
  - tiff:
      type: file
      description: A tiff file with gridlines filled based on consecutive gaussian blurring.
      pattern: "*.{tiff}"
authors:
  - "@ViriatoII"
  - "@flowuenne"
maintainers:
  - "@ViriatoII"
  - "@flowuenne"
