From 88936d503bdd96066687c78a63b05d4515722601 Mon Sep 17 00:00:00 2001
From: Jalil Nourisa <jalil.nourisa@gmail.com>
Date: Tue, 26 Nov 2024 22:30:25 +0100
Subject: [PATCH] scsgl added back

---
 src/methods/multi_omics/scglue/config.vsh.yaml     | 14 +++++++-------
 src/methods/single_omics/scenic/script.py          |  1 +
 .../scsgl/{config.novsh.yaml => config.vsh.yaml}   |  0
 src/methods/single_omics/scsgl/script.py           |  6 +++---
 4 files changed, 11 insertions(+), 10 deletions(-)
 rename src/methods/single_omics/scsgl/{config.novsh.yaml => config.vsh.yaml} (100%)

diff --git a/src/methods/multi_omics/scglue/config.vsh.yaml b/src/methods/multi_omics/scglue/config.vsh.yaml
index c34b49ac3..98b94d72c 100644
--- 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
index d8965042b..a0b995ef7 100644
--- 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/src/methods/single_omics/scsgl/config.novsh.yaml b/src/methods/single_omics/scsgl/config.vsh.yaml
similarity index 100%
rename from src/methods/single_omics/scsgl/config.novsh.yaml
rename to src/methods/single_omics/scsgl/config.vsh.yaml
diff --git a/src/methods/single_omics/scsgl/script.py b/src/methods/single_omics/scsgl/script.py
index 11cc9cc5d..210c18bb0 100644
--- a/src/methods/single_omics/scsgl/script.py
+++ b/src/methods/single_omics/scsgl/script.py
@@ -13,7 +13,7 @@
 
 ## 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
@@ -21,8 +21,8 @@
 ## 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