update readme

README.md

@@ -1,47 +1,181 @@
-# Task Template
+# Spatial Simulators
+
+
+<!--
+This file is automatically generated from the tasks's api/*.yaml files.
+Do not edit this file directly.
+-->
+
+Assessing the quality of spatial transcriptomics simulators
+
+Repository:
+[openproblems-bio/task_spatial_simulators](https://github.com/openproblems-bio/task_spatial_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.
+
+## Authors & contributors
+
+| name              | roles              |
+|:------------------|:-------------------|
+| Xiaoqi Liang      | author, maintainer |
+| Yue Cao           | author             |
+| Jean Yang         | author             |
+| Robrecht Cannoodt | contributor        |
+| Sai Nirmayi Yasa  | contributor        |
+
+## API
+
+``` mermaid
+flowchart LR
+  comp_process_datasets[/"Process Dataset"/]
+  file_dataset_sc("Single-Cell Dataset")
+  file_dataset_sp("Spatial Dataset")
+  comp_metric[/"Metric"/]
+  comp_control_method[/"Control Method"/]
+  comp_method[/"Method"/]
+  file_score("Score")
+  file_simulated_dataset("Solution")
+  comp_process_datasets-->file_dataset_sc
+  comp_process_datasets-->file_dataset_sp
+  file_dataset_sc---comp_metric
+  file_dataset_sp---comp_metric
+  file_dataset_sp---comp_control_method
+  file_dataset_sp---comp_method
+  comp_metric-->file_score
+  comp_control_method-->file_simulated_dataset
+  comp_method-->file_simulated_dataset
+  file_simulated_dataset---comp_metric
+```
 
-This repo is a template to create a new task for the OpenProblems v2. This repo contains several example files and components that can be used when updated with the task info.
+## Component type: Process Dataset
 
-> [!WARNING] 
-> This README will be overwritten when performing the `create_task_readme` script.
+Preprocessing of spatial transcriptomics and single-cell transcriptomics
+datasets.
 
-## Create a repository from this template
+Arguments:
 
-> [!IMPORTANT] 
-> Before creating a new repository, make sure you are part of the openProblems task team. This will be done when you create an issue for the task and you got the go ahead to create the task.
-> For more information on how to create a new task, check out the [Create a new task](https://openproblems.bio/documentation/create_task/) documentation.
+<div class="small">
 
-The instructions below will guide you through creating a new repository from this template ([creating-a-repository-from-a-template](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template#creating-a-repository-from-a-template)).
+| Name | Type | Description |
+|:---|:---|:---|
+| `--input_sc` | `file` | NA. |
+| `--input_sp` | `file` | NA. |
+| `--output_sc` | `file` | (*Output*) An unprocessed single-cell dataset as output by a dataset loader. Default: `$id/output_sc.h5ad`. |
+| `--output_sp` | `file` | (*Output*) An unprocessed spatial dataset as output by a dataset loader. Default: `$id/output_sp.h5ad`. |
+| `--dataset_id` | `string` | NA. |
+| `--dataset_name` | `string` | NA. |
+| `--dataset_url` | `string` | (*Optional*) NA. |
+| `--dataset_reference` | `string` | (*Optional*) NA. |
+| `--dataset_summary` | `string` | NA. |
+| `--dataset_description` | `string` | NA. |
+| `--dataset_organism` | `string` | NA. |
 
+</div>
 
-* Click the "Use this template" button on the top right of the repository.
-* Use the Owner dropdown menu to select the `openproblems-bio` account.
-* Type a name for your repository (task_...), and a description.
-* Set the repository visibility to public.
-* Click "Create repository from template".
+## File format: Single-Cell Dataset
 
-## Clone the repository
+An unprocessed single-cell dataset as output by a dataset loader.
 
-To clone the repository with the submodule files, you can use the following command:
+Example file: `resources_test/datasets/MOBNEW/dataset_sc.h5ad`
 
-```bash
-git clone --recursive [email protected]:openproblems-bio/task_spatial_simulators.git
-```
+Description:
 
-If you already cloned the repository and forgot to use the `--recursive` flag, you can use the following command to update the submodules:
+This dataset contains raw counts and metadata as output by a dataset
+loader.
 
-```bash
-git submodule update --init --recursive
-```
+The format of this file is derived from the [CELLxGENE schema
+v4.0.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/4.0.0/schema.md).
 
-Once you have cloned the repository, you can start download the test resources using the following command:
+## File format: Spatial Dataset
 
-```bash
-scripts/download_resources.sh
-```
+An unprocessed spatial dataset as output by a dataset loader.
+
+Example file: `resources_test/datasets/MOBNEW/dataset_sp.h5ad`
+
+Description:
+
+This dataset contains raw counts and metadata as output by a dataset
+loader.
+
+The format of this file is derived from the [CELLxGENE schema
+v4.0.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/4.0.0/schema.md).
+
+## Component type: Metric
+
+A metric.
+
+Arguments:
+
+<div class="small">
+
+| Name | Type | Description |
+|:---|:---|:---|
+| `--input_spatial_dataset` | `file` | An unprocessed spatial dataset as output by a dataset loader. |
+| `--input_singlecell_dataset` | `file` | An unprocessed single-cell dataset as output by a dataset loader. |
+| `--input_simulated_dataset` | `file` | The solution for the test data. |
+| `--output` | `file` | (*Output*) File indicating the score of a metric. |
+
+</div>
+
+## Component type: Control Method
+
+A control method.
+
+Arguments:
+
+<div class="small">
+
+| Name | Type | Description |
+|:---|:---|:---|
+| `--input` | `file` | (*Optional*) An unprocessed spatial dataset as output by a dataset loader. |
+| `--output` | `file` | (*Output*) The solution for the test data. |
+
+</div>
+
+## Component type: Method
+
+A method.
+
+Arguments:
+
+<div class="small">
+
+| Name | Type | Description |
+|:---|:---|:---|
+| `--input` | `file` | (*Optional*) An unprocessed spatial dataset as output by a dataset loader. |
+| `--base` | `string` | (*Optional*) NA. Default: `domain`. |
+| `--base` | `string` | (*Optional*) NA. Default: `domain`. |
+| `--output` | `file` | (*Output*) The solution for the test data. |
+
+</div>
+
+## File format: Score
+
+File indicating the score of a metric.
+
+Example file: `resources/score.h5ad`
+
+## File format: Solution
 
-## What to do next
+The solution for the test data
 
-Check out the [instructions](common/INSTRUCTIONS.md) for more information on how to update the example files and components. These instructions also contain information on how to build out the task and basic commands.
+Example file: `resources_test/datasets/MOBNEW/simulated_dataset.h5ad`
 
-For more information on the OpenProblems v2, check out the [Documentation](https://openproblems.bio/documentation/).

src/api/comp_process_datasets.yaml

@@ -23,14 +23,14 @@ argument_groups:
 
   - name: Outputs
     arguments:
-      - type: file
-        name: --output_sc
+      - name: --output_sc
+        __merge__: file_dataset_sc.yaml
         description: Processed single-cell dataset
         direction: output
         required: true
         default: '$id/output_sc.h5ad'
-      - type: file
-        name: --output_sp
+      - name: --output_sp
+        __merge__: file_dataset_sp.yaml
         description: Processed spatial dataset
         direction: output
         required: true