task_spatial_trajectory_inference/_viash.yaml at main · openproblems-bio/task_spatial_trajectory_inference · GitHub

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viash_version: 0.9.4

name: task_spatial_trajectory_inference
organization: openproblems-bio
version: dev

license: MIT
keywords: [single-cell, openproblems, benchmark, spatial, trajectory inference]
links:
  issue_tracker: https://github.com/openproblems-bio/task_spatial_trajectory_inference/issues
  repository: https://github.com/openproblems-bio/task_spatial_trajectory_inference
  docker_registry: ghcr.io


label: Spatial Trajectory Inference
summary: Predicting the spatial trajectory of cells in a tissue based on spatial transcriptomics data.
description:

  Spatial transcriptomics preserves each cell's physical position alongside its expression profile, enabling pseudotime prediction using 2D spatial context.
  Different methods make different assumptions about resolution, input format, and output, and are further complicated by spatial batch effects not present in dissociated single-cell data.
  While dynbenchmark resolved this comparison problem for non-spatial trajectory inference methods, no equivalent standardized benchmark exists for spatial pseudotime prediction, and existing method papers are validated only against each other or qualitative marker trends rather than tissues with independently known trajectories.

  This task benchmarks pseudotime prediction methods on 2D tissue datasets with well-characterized ground-truth spatial axes.
  Input data consists of AnnData objects containing 2D spatial transcriptomics data with spatial coordinates.
  The output is a set of quantitative metric scores comparing each method's predicted pseudotime against ground truth, capturing both trajectory accuracy and preservation of relevant biological information.

# A list of references to relevant literature. Each reference should be a DOI or a bibtex entry
references:
  doi:
    - 10.21203/rs.3.rs-4181617/v1
  # bibtex:
  #   - |
  #     @article{doe_2021_template,
  #       doi = {10.21203/rs.3.rs-4181617/v1},
  #       url = {https://doi.org/10.21203/rs.3.rs-4181617/v1},
  #       author = {Doe, John},
  #       title = {A template for creating new tasks},
  #       publisher = {Research Square},
  #       year = {2021},
  #     }

info:
  image: The name of the image file to use for the component on the website.
  test_resources:
    - type: s3
      path: s3://openproblems-data/resources_test/common/
      dest: resources_test/common
    - type: s3
      path: s3://openproblems-data/resources_test/task_spatial_trajectory_inference/
      dest: resources_test/task_spatial_trajectory_inference

authors:
  - name: Chit Tong Lio
    roles: [ "author", "maintainer" ]
    info:
      github: yollct
      orcid: 0000-0003-2297-831X
      email: [email protected]
  - name: Seo Hyon Kim
    roles: [ "author", "maintainer" ]
    info:
      github: seohyonkim
      orcid: 0009-0007-3062-4681
      email: [email protected]
  - name: Wenjia Zhong
    roles: [ "author", "maintainer" ]
    info:
      github: Wenjia218
      orcid: 0009-0009-1594-8009
      email: [email protected]
  - name: Luisa Katharina Bender
    roles: [ "author", "maintainer" ]
    info:
      github: luisabender
      orcid: 0009-0001-8753-7307
      email: [email protected]
  - name: Florian Röckl
    roles: [ "author", "maintainer" ]
    info:
      github: floro5
      orcid: 0009-0009-6050-890X
      email: [email protected]
  - name: Jonathan Unger
    roles: [ "author", "maintainer" ]
    info:
      github: Jonique02
      orcid: 0009-0009-5022-2975
      email: [email protected]

# Step 7: Remove all of the comments of the steps you completed

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" }

repositories:
  - name: openproblems
    type: github
    repo: openproblems-bio/openproblems
    tag: build/main # Step 8: Set this to the latest release

# Step 9: High five yourself!