workflow updated

openproblems-bio · Sep 15, 2024 · a60f0ef · a60f0ef
1 parent c1adbbd
commit a60f0ef
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/src/methods/multi_omics/scglue/main.py b/src/methods/multi_omics/scglue/main.py
@@ -239,7 +239,7 @@ def prune_grn(par):
     par['genes_vs_motifs_500'] = 'output/scenic/databases/hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather'
     par['genes_vs_motifs_10k'] =  'output/scenic/databases/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather'
     par['motif_annotation'] = 'output/scenic/databases/motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl'
-    
+
     command = [
         "pyscenic", "ctx",
         f"{par['temp_dir']}/draft_grn.csv",
@@ -253,7 +253,9 @@ def prune_grn(par):
         "--nes_threshold", "2",
         "--mask_dropouts",
         "--min_genes", "1",
-        "--num_workers", f"{par['num_workers']}"
+        "--num_workers", f"{par['num_workers']}",
+        "--cell_id_attribute", "obs_id",
+        "--gene_attribute", "name"
     ]
 
     result = subprocess.run(command, check=True)

diff --git a/src/workflows/run_benchmark_single_omics/main.nf b/src/workflows/run_benchmark_single_omics/main.nf
@@ -18,8 +18,6 @@ workflow run_wf {
     genie3,
     grnboost2,
     ppcor,
-    scsgl,
-    tigress,
     scgpt,
     scenic
   ]