_viash.yaml

name: task_cell_cell_communication
version: 0.1.0

# package metadata
label: Cell-Cell Communication
summary: Predicting cell-cell interactions between source cell types and target cell types.
description: |
  The growing availability of single-cell data has sparked an increased interest in the inference of cell-cell communication (CCC),
  with an ever-growing number of computational tools developed for this purpose.
  
  Different tools propose distinct preprocessing steps with diverse scoring functions that are challenging to compare and evaluate.
  Furthermore, each tool typically comes with its own set of prior knowledge. To harmonize these,
  Dimitrov et al recently developed the [LIANA+](https://github.com/saezlab/liana-py) framework, which was used as a foundation for this task.
  
  The challenges in evaluating the tools are further exacerbated by the lack of a gold standard to benchmark the performance of CCC
  methods. In an attempt to address this, Dimitrov et al use alternative data modalities, including the spatial proximity of cell types
  and downstream cytokine activities, to generate an inferred ground truth. However, these modalities are only approximations of
  biological reality and come with their own assumptions and limitations. In time, the inclusion of more datasets with known ground
  truth interactions will become available, from which the limitations and advantages of the different CCC methods will be better understood.
  This subtask evaluates methods in their ability to predict interactions between spatially-adjacent source cell types and target
  cell types. This subtask focuses on the prediction of interactions from steady-state, or single-context, single-cell data.
license: MIT
keywords: [single-cell, cell-cell communication, openproblems, benchmark]

references:
  doi:
    # Dimitrov, D., Türei, D., Garrido-Rodriguez, M. et al. Comparison of methods and resources
    # for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022).
    # https://doi.org/10.1038/s41467-022-30755-0
    - 10.1038/s41467-022-30755-0
    # Dimitrov, D., Schäfer, P.S.L., Farr, E. et al. LIANA+ provides an all-in-one framework for
    # cell-cell communication inference. Nat Cell Biol 26, 1613–1622 (2024).
    # https://doi.org/10.1038/s41556-024-01469-w
    - 10.1038/s41556-024-01469-w

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

# technical settings
organization: openproblems-bio
viash_version: 0.9.0
info:
  image: "thumbnail.svg"
  test_resources:
    - type: s3
      path: s3://openproblems-data/resources_test/common/singlecell_broadinstitute_scp2167_human_brain/
      dest: resources_test/common/singlecell_broadinstitute_scp2167_human_brain/
    - type: s3
      path: s3://openproblems-data/resources_test/task_cell_cell_communication
      dest: resources_test/task_cell_cell_communication

authors:
  - name: Daniel Dimitrov
    roles: [ maintainer, author ]
    info:
      github: dbdimitrov
  - name: "Scott Gigante"
    roles: [ contributor ]
    info:
      github: scottgigante
      orcid: "0000-0002-4544-2764"
  - name: Robrecht Cannoodt
    roles: [ contributor ]
    info:
      github: rcannood
      orcid: "0000-0003-3641-729X"
  - name: Vishnuvasan Raghuraman
    roles: [ contributor ]
    info:
      github: vishnu-vasan

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
  - name: core
    type: github
    repo: openproblems-bio/core
    tag: build/main
    path: viash/core