Merge branch 'main' of https://github.com/openproblems-bio/task_spati…

…al_simulators

_viash.yaml

@@ -1,22 +1,81 @@
-viash_version: 0.9.0-RC6
+viash_version: 0.9.0-RC7
 
 name: task_spatial_simulators
 organization: openproblems-bio
-description: |
-  An OpenProblems benchmark task of spatial simulators.
+version: dev
 license: MIT
-keywords: [single-cell, openproblems, benchmark, spatial simulation]
+
+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
 
-version: dev
+repositories:
+  - name: openproblems_v2
+    type: github
+    repo: openproblems-bio/openproblems-v2
+    tag: main_build
 
 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" }

src/api/task_info.yaml

@@ -1,3 +1,5 @@
+# todo: this file will be removed in the near future.
+# use _viash.yaml instead.
 name: task_spatial_simulators
 label: spatial transcriptomics, single-cell, openproblems, benchmark, spatial simulation
 summary: Benchmark study of spatial simulation models.

src/metrics/ks_statistic_scFeatures/config.vsh.yaml → src/metrics/ks_statistic_sc_features/config.vsh.yaml

@@ -1,6 +1,6 @@
 __merge__: ../../api/comp_metric.yaml
 
-name: ks_statistic_scFeatures
+name: ks_statistic_sc_features
 
 info:
   metrics:
@@ -64,6 +64,7 @@ engines:
           - r-cran-ks
           - r-cran-resample
           - r-cran-reshape2
+          - r-bioc-scater
 
 runners:
   - type: executable

src/workflows/run_benchmark/config.vsh.yaml

@@ -62,10 +62,5 @@ dependencies:
   - name: methods/symsim
   - name: methods/zinbwave
   - name: metrics/ks_statistic_gene_cell
-repositories:
-  - name: openproblems_v2
-    type: github
-    repo: openproblems-bio/openproblems-v2
-    tag: main_build
 runners:
   - type: nextflow