gpu added to single omics benchmark

openproblems-bio · Sep 9, 2024 · 3379386 · 3379386
1 parent 886e3c1
commit 3379386
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/scripts/run_benchmark_single_omics.sh b/scripts/run_benchmark_single_omics.sh
@@ -48,7 +48,7 @@ HERE
 #     --main-script target/nextflow/workflows/run_benchmark_single_omics/main.nf `
 #     --workspace 53907369739130 `
 #     --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
-#     --params-file ./params/single_omics_all_test.yaml `
+#     --params-file ./params/single_omics_scgpt.yaml `
 #     --config src/common/nextflow_helpers/labels_tw.config
 
 
diff --git a/src/methods/single_omics/scgpt/config.vsh.yaml b/src/methods/single_omics/scgpt/config.vsh.yaml
@@ -39,4 +39,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [midtime, midmem, midcpu]
+      label: [midtime, midmem, midcpu, gpu]
diff --git a/src/process_data/perturbation/batch_correction_seurat/config.vsh.yaml b/src/process_data/perturbation/batch_correction_seurat/config.vsh.yaml
@@ -50,7 +50,7 @@ platforms:
     image: janursa/batch_correction_seurat:latest
     setup:
       - type: python
-        packages: [anndata==0.10.9]
+        packages: [anndata]
 
   - type: native
   - type: nextflow

diff --git a/src/workflows/run_benchmark_single_omics/config.vsh.yaml b/src/workflows/run_benchmark_single_omics/config.vsh.yaml
@@ -102,4 +102,4 @@ functionality:
 platforms:
   - type: nextflow
     directives:
-      label: [ threedaystime, midmem, highcpu]
+      label: [ threedaystime, midmem, highcpu, gpu]