task_ist_preprocessing/src/methods_transcript_assignment/fastreseg/config.vsh.yaml at d529236787ebf3a9b1da94628b11a4cc393ef2b8 · openproblems-bio/task_ist_preprocessing · GitHub

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__merge__: /src/api/comp_method_transcript_assignment.yaml

name: fastreseg
label: "fastReseg transcript assignment"
summary: "Spatial segmentation correction using fastReseg method"
description: |
  fastReseg is an R package designed to enhance the precision of cell segmentation in spatial transcriptomics by
  leveraging transcriptomic data to correct and refine initial image-based segmentation results.
links:
  documentation: "https://github.com/openproblems-bio/task_ist_preprocessing"
  repository: "https://github.com/openproblems-bio/task_ist_preprocessing"
references:
  doi: "10.1038/s41598-025-08733-5"


#arguments:
#  - name: --transcripts_key
#    type: string
#    default: "transcripts"
#    description: "Key for transcripts in the points layer"
#  - name: --coordinate_system
#    type: string
#    default: "global"
#    description: "Coordinate system for the transcripts"


resources:
  - type: bash_script
    path: orchestrator.sh
  - type: python_script
    path: input.py
  - type: r_script
    path: script.R
  - type: python_script
    path: output.py

engines:
  - type: docker
    image: openproblems/base_python:1
    setup:
      - type: apt
        packages:
          - libv8-dev
          - libudunits2-dev
          - libabsl-dev
          - gdal-bin
          - libgdal-dev
          - r-base
      - type: r
        packages:
          - devtools
          - terra
          - Matrix
          - dbscan
          - igraph
          - matrixStats
          - codetools
          - data.table
          # Add other CRAN packages here
        github:
          # Add GitHub packages here if needed
          - Nanostring-Biostats/FastReseg
      #- type: python
      #  github:
      #    - openproblems-bio/core#subdirectory=packages/python/openproblems
    __merge__:
      - /src/base/setup_txsim_partial.yaml
      - /src/base/setup_spatialdata_partial.yaml
  - type: native

runners:
  - type: executable
  - type: nextflow
    directives:
      label: [ midtime, midcpu, midmem ]


##macOS workaround: export DOCKER_DEFAULT_PLATFORM=linux/amd64