Merge branch 'openproblems-bio:main' into main

Author: EpigeneMax

CHANGELOG.md

@@ -1,8 +1,21 @@
 # task_batch_integration devel
 
+## New functionality
+
+* Added `metrics/kbet_pg` and `metrics/kbet_pg_label` components (PR #52).
+* Added `method/drvi` component (PR #61).
+
+* Added `ARI_batch` and `NMI_batch` to `metrics/clustering_overlap` (PR #68).
+
 ## Minor changes
 
 * Un-pin the scPRINT version and update parameters (PR #51)
+* Update scPRINT to better handle large datasets, including a new default model (PR #54)
+
+## Bug fixes
+
+* Update scPRINT to use latest stable version (PR #70)
+* Fix kbet dependencies to numpy<2 and scipy<=1.13 (PR #78).
 
 # task_batch_integration 2.0.0
 

CONTRIBUTING.md

@@ -141,12 +141,14 @@ viash ns test --parallel
 
 ### Running the benchmark
 
-To run the benchmark, you can use the following command:
+To locally test the benchmark workflow, you can use the following command:
 
 ```bash
-scripts/run_benchmark/run.sh
+scripts/run_benchmark/run_test_local.sh
 ```
 
+Other scripts in `scripts/run_benchmark/` provide commands for testing on Seqera Cloud and for production runs. 
+
 ## Debugging nf-tower runs
 
 The actual benchmark is run on the [nf-tower platform](https://cloud.seqera.io/orgs/openproblems-bio/workspaces/openproblems-bio/watch).

_viash.yaml

@@ -1,4 +1,4 @@
-viash_version: 0.9.0
+viash_version: 0.9.4
 
 name: task_batch_integration
 organization: openproblems-bio

src/control_methods/embed_cell_types/config.vsh.yaml

@@ -13,7 +13,7 @@ resources:
   - path: /src/control_methods/utils.py
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
 runners:
   - type: executable
   - type: nextflow

src/control_methods/embed_cell_types_jittered/config.vsh.yaml

@@ -19,7 +19,7 @@ resources:
   - path: /src/control_methods/utils.py
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
 runners:
   - type: executable
   - type: nextflow

src/control_methods/no_integration/config.vsh.yaml

@@ -12,7 +12,7 @@ resources:
   - path: /src/utils/read_anndata_partial.py
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
 runners:
   - type: executable
   - type: nextflow

src/control_methods/no_integration_batch/config.vsh.yaml

@@ -12,7 +12,7 @@ resources:
   - path: /src/utils/read_anndata_partial.py
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
 runners:
   - type: executable
   - type: nextflow

src/control_methods/shuffle_integration/config.vsh.yaml

@@ -12,7 +12,7 @@ resources:
   - path: /src/control_methods/utils.py
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
 runners:
   - type: executable
   - type: nextflow

src/control_methods/shuffle_integration_by_batch/config.vsh.yaml

@@ -12,7 +12,7 @@ resources:
   - path: /src/control_methods/utils.py
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
 runners:
   - type: executable
   - type: nextflow

src/control_methods/shuffle_integration_by_cell_type/config.vsh.yaml

@@ -12,7 +12,7 @@ resources:
   - path: /src/control_methods/utils.py
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
 runners:
   - type: executable
   - type: nextflow