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

Author: littlecabiria

common

@@ -1,7 +1,7 @@
 __merge__: ../../api/comp_method.yaml
 
-name: scdesign3
-label: scDesign3
+name: scdesign3_nb
+label: scDesign3 (NB)
 summary: A probabilistic model that unifies the generation and inference for single-cell and spatial omics data
 description: |
   scDesign3 offers a probabilistic model that unifies the generation and inference

src/methods/scdesign3/config.vsh.yaml renamed to src/methods/scdesign3_nb/config.vsh.yaml

@@ -0,0 +1,51 @@
+__merge__: ../../api/comp_method.yaml
+
+name: scdesign3_poisson
+label: scDesign3 (Poisson)
+summary: A probabilistic model that unifies the generation and inference for single-cell and spatial omics data
+description: |
+  scDesign3 offers a probabilistic model that unifies the generation and inference
+  for single-cell and spatial omics data. The model's interpretable parameters and
+  likelihood enable scDesign3 to generate customized in silico data and unsupervisedly
+  assess the goodness-of-fit of inferred cell latent structures (for example, clusters,
+  trajectories and spatial locations).
+references:
+  doi: 10.1038/s41587-023-01772-1
+links:
+  documentation: https://www.bioconductor.org/packages/release/bioc/html/scDesign3.html
+  repository: https://github.com/SONGDONGYUAN1994/scDesign3
+
+arguments:
+  - name: "--family"
+    type: "string"
+    default: poisson
+    description: |
+      A string or a vector of strings of the marginal distribution. Must be one of 'binomial',
+      'poisson', 'nb', 'zip', 'zinb' or 'gaussian', which represent 'poisson distribution',
+      'negative binomial distribution', 'zero-inflated poisson distribution',
+      'zero-inflated negative binomial distribution', and 'gaussian distribution'
+      respectively.
+    choices: [binomial, poisson, nb, zip, zinb, gaussian]
+  - name: "--usebam"
+    type: boolean
+    default: false
+    description: "Use `bam` for acceleration."
+
+resources:
+  - type: r_script
+    path: ../scdesign3_nb/script.R
+
+engines:
+  - type: docker
+    image: openproblems/base_r:1.0.0
+    setup:
+      - type: apt
+        packages: [r-bioc-singlecellexperiment, git]
+      - type: r
+        github: SONGDONGYUAN1994/scDesign3
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [hightime, midmem, midcpu]

src/methods/scdesign3/script.R renamed to src/methods/scdesign3_nb/script.R

@@ -81,8 +81,9 @@ engines:
         packages:
           - numpy
           - scikit-learn
-          - squidpy 
+          - squidpy
           - scipy
+          - dask==2024.12.1
 
 runners:
   - type: executable

src/methods/scdesign3_poisson/config.vsh.yaml

@@ -49,7 +49,8 @@ dependencies:
   - name: utils/extract_uns_metadata
     repository: openproblems
   - name: methods/scdesign2
-  - name: methods/scdesign3
+  - name: methods/scdesign3_nb
+  - name: methods/scdesign3_poisson
   - name: methods/sparsim
   - name: methods/splatter
   - name: methods/srtsim

src/metrics/ks_statistic_spatial/config.vsh.yaml

@@ -8,7 +8,8 @@ workflow auto {
 // construct list of methods
 methods = [
   scdesign2,
-  scdesign3,
+  scdesign3_nb,
+  scdesign3_poisson,
   sparsim,
   splatter,
   srtsim,