scsgl added back

openproblems-bio · Nov 26, 2024 · 88936d5 · 88936d5
1 parent 608673a
commit 88936d5
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Showing 4 changed files with 11 additions and 10 deletions.
diff --git a/src/methods/multi_omics/scglue/config.vsh.yaml b/src/methods/multi_omics/scglue/config.vsh.yaml
@@ -41,13 +41,13 @@ functionality:
 
 platforms:
   - type: docker
-    # image: janursa/scglue:19-08-2024
-    image: nvcr.io/nvidia/pytorch:24.06-py3
-    setup:
-      - type: python
-        packages: [ scglue==0.3.2, pyscenic==0.12.1, numpy==1.23.4, scanpy, networkx, pyarrow, cytoolz, scikit-misc, cuda-python, faiss-gpu]
-      - type: apt
-        packages: [bedtools]
+    image: janursa/scglue:19-08-2024
+    # image: nvcr.io/nvidia/pytorch:24.06-py3
+    # setup:
+    #   - type: python
+    #     packages: [ scglue==0.3.2, pyscenic==0.12.1, numpy==1.23.4, scanpy, networkx, pyarrow, cytoolz, scikit-misc, cuda-python, faiss-gpu]
+    #   - type: apt
+    #     packages: [bedtools]
 
   - type: native
   - type: nextflow

diff --git a/src/methods/single_omics/scenic/script.py b/src/methods/single_omics/scenic/script.py
@@ -143,6 +143,7 @@ def main(par):
   par['expression_data'] = os.path.join(par['temp_dir'], "expression_data.tsv")
   par['regulons'] = f"{par['temp_dir']}/regulons.csv"
 
+  download_prior(par)
   format_data(par)
   run_grn(par)
   prune_grn(par)

diff --git a/...hods/single_omics/scsgl/config.novsh.yaml → ...ethods/single_omics/scsgl/config.vsh.yaml b/...hods/single_omics/scsgl/config.novsh.yaml → ...ethods/single_omics/scsgl/config.vsh.yaml
diff --git a/src/methods/single_omics/scsgl/script.py b/src/methods/single_omics/scsgl/script.py
@@ -13,16 +13,16 @@
 
 ## VIASH START
 par = {
-  'multiomics_rna': 'resources/resources_test/grn-benchmark/multiomics_rna.h5ad',
+  'rna': 'resources/resources_test/grn-benchmark/multiomics_rna.h5ad',
   'prediction': 'output/scsgl/prediction.csv',
   'temp_dir': 'output/scsgl',
   'max_n_links': 50000
 }
 ## VIASH END
 
 # Load scRNA-seq data
-adata_rna = anndata.read_h5ad(par['multiomics_rna'])
-gene_names = adata_rna.var.gene_ids.index.to_numpy()
+adata_rna = anndata.read_h5ad(par['rna'])
+gene_names = adata_rna.var_names
 X = adata_rna.X.toarray() if scipy.sparse.issparse(adata_rna.X) else adata_rna.X
 
 # Import pysrc locally