_viash.yaml

viash_version: 0.9.0

name: task_spatial_simulators
organization: openproblems-bio
version: dev
license: MIT

label: Spatial Simulators
summary: Assessing the quality of spatial transcriptomics simulators
description: |
  Computational methods for spatially resolved transcriptomics (SRT) are frequently developed 
  and assessed through data simulation. The effectiveness of these evaluations relies on the 
  simulation methods' ability to accurately reflect experimental data. However, a systematic 
  evaluation framework for spatial simulators is lacking. Here, we present SpatialSimBench, 
  a comprehensive evaluation framework that assesses 13 simulation methods using 10 distinct 
  STR datasets.

  The research goal of this benchmark is to systematically evaluate and compare the
  performance of various simulation methods for spatial transcriptomics (ST) data.
  It aims to address the lack of a comprehensive evaluation framework for spatial simulators
  and explore the feasibility of leveraging existing single-cell simulators for ST data.
  The experimental setup involves collecting public spatial transcriptomics datasets and
  corresponding scRNA-seq datasets.
  The spatial and scRNA-seq datasets can originate from different study but should consist
  of similar cell types from similar tissues.
keywords: [single-cell, spatial transcriptomics, in-silico, spatial simulation]
references:
  doi:
    # Multi-task benchmarking of spatially resolved gene expression simulation models
    # Xiaoqi Liang, Yue Cao, Jean Yee Hwa Yang
    # bioRxiv 2024.05.29.596418; doi: https://doi.org/10.1101/2024.05.29.596418 
    - 10.1101/2024.05.29.596418

authors:
  - name: Xiaoqi Liang
    roles: [author, maintainer]
    info:
      orcid: 0009-0004-9625-1441
      github: littlecabiria
  - name: Yue Cao
    roles: [author]
    info:
      orcid: 0000-0002-2356-4031
      github: ycao6928
  - name: Jean Yang
    roles: [author]
    info:
      orcid: 0000-0002-5271-2603
      github: jeany21
  - name: Robrecht Cannoodt
    roles: [contributor]
    info:
      github: rcannood
      orcid: 0000-0003-3641-729X
  - name: Sai Nirmayi Yasa
    roles: [contributor]
    info: 
      github: sainirmayi
      orcid: 0009-0003-6319-9803

links:
  issue_tracker: https://github.com/openproblems-bio/task_spatial_simulators/issues
  repository: https://github.com/openproblems-bio/task_spatial_simulators
  docker_registry: ghcr.io

info:
  # image: thumbnail.svg

  test_resources:
    - type: s3
      path: s3://openproblems-data/resources_test/task_spatial_simulators
      dest: resources_test

repositories:
  - name: openproblems
    type: github
    repo: openproblems-bio/openproblems
    tag: build/main

config_mods: |
  .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
  .runners[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'"