Add scGPT to benchmark workflow

openproblems-bio · Nov 5, 2024 · c4dfc2f · c4dfc2f
1 parent 1241309
commit c4dfc2f
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diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
@@ -94,6 +94,7 @@ dependencies:
   - name: methods/scanorama
   - name: methods/scanvi
   - name: methods/scimilarity
+  - name: methods/scgpt
   - name: methods/scvi
   # metrics
   - name: metrics/asw_batch

diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
@@ -31,6 +31,7 @@ methods = [
   scimilarity.run(
     args: [model: file("s3://openproblems-work/cache/scimilarity-model_v1.1.tar.gz")]
   ),
+  scgpt,
   scvi
 ]
-Original file line number
+Diff line change
@@ Expand Up / @@ -31,6 +31,7 @@ methods = [ @@
       scimilarity.run(
         args: [model: file("s3://openproblems-work/cache/scimilarity-model_v1.1.tar.gz")]
       ),
+      scgpt,
       scvi
     ]
@@ Expand Down @@