diff --git a/modules/local/adata/extend/templates/extend.py b/modules/local/adata/extend/templates/extend.py
index d01ec0f1..4ebb339f 100644
--- a/modules/local/adata/extend/templates/extend.py
+++ b/modules/local/adata/extend/templates/extend.py
@@ -38,6 +38,10 @@ def load_pickle_or_csv(path):
     df = load_pickle_or_csv(path).reindex(adata.var_names)
     adata.var = pd.concat([adata.var, df], axis=1)
 
+# Ensure 'highly_variable' is boolean if present
+if "highly_variable" in adata.var:
+    adata.var["highly_variable"] = adata.var["highly_variable"].astype(bool)
+
 for path in obsm_paths:
     df = pd.read_pickle(path).reindex(adata.obs_names)
     adata.obsm[simple_name(path)] = np.float32(df.to_numpy())
diff --git a/modules/local/adata/readrds/environment.yml b/modules/local/adata/readrds/environment.yml
index d2e3a91e..e3b873c8 100644
--- a/modules/local/adata/readrds/environment.yml
+++ b/modules/local/adata/readrds/environment.yml
@@ -6,3 +6,5 @@ dependencies:
   - bioconda::anndata2ri=1.3.2
   - conda-forge::anndata=0.11.1
   - conda-forge::r-seurat=5.1.0
+  - bioconda::bioconductor-singlecellexperiment=1.24.0
+  - conda-forge::rpy2=3.5.11
diff --git a/modules/local/adata/readrds/main.nf b/modules/local/adata/readrds/main.nf
index 12b6f740..9c2a9fbe 100644
--- a/modules/local/adata/readrds/main.nf
+++ b/modules/local/adata/readrds/main.nf
@@ -4,8 +4,8 @@ process ADATA_READRDS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/anndata2ri_bioconductor-singlecellexperiment_anndata_r-seurat:c4b75a61a89ec006':
-        'community.wave.seqera.io/library/anndata2ri_bioconductor-singlecellexperiment_anndata_r-seurat:5fae42aabf7a1c5f' }"
+        'oras://community.wave.seqera.io/library/anndata2ri_bioconductor-singlecellexperiment_anndata_r-seurat_rpy2:5e5acc8a27b2f90a':
+        'community.wave.seqera.io/library/anndata2ri_bioconductor-singlecellexperiment_anndata_r-seurat_rpy2:5e785d9c16504ed6' }"
 
     input:
     tuple val(meta), path(rds)
diff --git a/modules/local/adata/readrds/templates/readrds.py b/modules/local/adata/readrds/templates/readrds.py
index 04180471..47344c26 100644
--- a/modules/local/adata/readrds/templates/readrds.py
+++ b/modules/local/adata/readrds/templates/readrds.py
@@ -4,6 +4,8 @@
 
 os.environ["TMPDIR"] = "."
 
+import importlib.metadata
+
 import anndata as ad
 import anndata2ri
 import rpy2
@@ -53,10 +55,10 @@ def format_yaml_like(data: dict, indent: int = 0) -> str:
 adata.write_h5ad("${prefix}.h5ad")
 
 versions = {
-    "${task.process}": {
+    "NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:LOAD_H5AD:ADATA_READRDS": {
         "anndata": ad.__version__,
         "anndata2ri": anndata2ri.__version__,
-        "rpy2": rpy2.__version__,
+        "rpy2": importlib.metadata.version("rpy2"),
         "pandas": pd.__version__,
         "seurat": seurat.__version__
     }
diff --git a/modules/local/adata/upsetgenes/templates/upsetplot.py b/modules/local/adata/upsetgenes/templates/upsetplot.py
index 5528e68d..8e2524e2 100644
--- a/modules/local/adata/upsetgenes/templates/upsetplot.py
+++ b/modules/local/adata/upsetgenes/templates/upsetplot.py
@@ -1,4 +1,4 @@
-#!/opt/conda/bin/python
+#!/usr/bin/env python
 
 import os
 import platform
diff --git a/modules/local/doublet_detection/doublet_removal/environment.yml b/modules/local/doublet_detection/doublet_removal/environment.yml
index 193d2281..2abbc38c 100644
--- a/modules/local/doublet_detection/doublet_removal/environment.yml
+++ b/modules/local/doublet_detection/doublet_removal/environment.yml
@@ -3,5 +3,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::anndata=0.11.1
-  - conda-forge::upsetplot=0.9.0
+  - python=3.11.9
+  - numpy=2.0.2
+  - scipy=1.14.1
+  - pandas=2.2.2
+  - matplotlib=3.8.4
+  - anndata=0.11.1
+  - upsetplot=0.9.0
diff --git a/modules/local/doublet_detection/doublet_removal/main.nf b/modules/local/doublet_detection/doublet_removal/main.nf
index c02fa190..23912fed 100644
--- a/modules/local/doublet_detection/doublet_removal/main.nf
+++ b/modules/local/doublet_detection/doublet_removal/main.nf
@@ -4,8 +4,8 @@ process DOUBLET_REMOVAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/anndata_upsetplot:922f36ea0326a629':
-        'community.wave.seqera.io/library/anndata_upsetplot:784e0f450da10178' }"
+        'oras://community.wave.seqera.io/library/anndata_matplotlib_numpy_pandas_pruned:a603920d55ea7f32':
+        'community.wave.seqera.io/library/anndata_matplotlib_numpy_pandas_pruned:9674070abcd72c6f' }"
 
     input:
     tuple val(meta), path(h5ad), path(predictions)
diff --git a/modules/local/doublet_detection/doublet_removal/templates/doublet_removal.py b/modules/local/doublet_detection/doublet_removal/templates/doublet_removal.py
index cbcfc2df..157d2a0f 100644
--- a/modules/local/doublet_detection/doublet_removal/templates/doublet_removal.py
+++ b/modules/local/doublet_detection/doublet_removal/templates/doublet_removal.py
@@ -1,4 +1,4 @@
-#!/opt/conda/bin/python
+#!/usr/bin/env python3
 
 import os
 import platform