Increase subsample dimensions (#392)

* Increase subsample dimensions Co-authored-by: Michaela Müller <[email protected]> * fix pancreas subsample error * force CI --------- Co-authored-by: Michaela Müller <[email protected]>
openproblems-bio · Mar 6, 2024 · 69140a2 · 69140a2
1 parent 28067c5
commit 69140a2
Show file tree

Hide file tree

Showing 5 changed files with 8 additions and 4 deletions.
diff --git a/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh b/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh
@@ -24,6 +24,8 @@ param_list:
     dataset_organism: mus_musculus
 
 normalization_methods: [log_cp10k]
+n_obs: 600
+n_vars: 1500
 output_dataset: '\$id/dataset.h5ad'
 output_meta: '\$id/dataset_metadata.yaml'
 output_state: '\$id/state.yaml'
@@ -39,6 +41,7 @@ HERE
 
 nextflow run . \
   -main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \
+  -c src/wf_utils/labels_ci.config \
   -profile docker \
   -params-file "/tmp/params.yaml"
 

diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh
@@ -40,6 +40,8 @@ nextflow run . \
   --seed 123 \
   --normalization_methods log_cp10k \
   --do_subsample true \
+  --n_obs 600 \
+  --n_var 1500 \
   --output_raw '$id/raw.h5ad' \
   --output_normalized '$id/normalized.h5ad' \
   --output_hvg '$id/hvg.h5ad' \
@@ -56,4 +58,4 @@ rm -r $DATASET_DIR/temp_*
 src/tasks/batch_integration/resources_test_scripts/process.sh
 src/tasks/denoising/resources_test_scripts/pancreas.sh
 src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh
-src/tasks/label_projection/resources_test_scripts/pancreas.sh
+src/tasks/label_projection/resources_test_scripts/pancreas.sh
diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml
@@ -1,7 +1,6 @@
 # use metric api spec
 __merge__: ../../api/comp_metric_embedding.yaml
 functionality:
-  status: disabled
   name: cell_cycle_conservation
   info:
     metrics:

diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml
@@ -77,7 +77,7 @@ functionality:
     - name: batch_integration/transformers/embed_to_graph
     - name: batch_integration/metrics/asw_batch
     - name: batch_integration/metrics/asw_label
-    # - name: batch_integration/metrics/cell_cycle_conservation
+    - name: batch_integration/metrics/cell_cycle_conservation
     - name: batch_integration/metrics/clustering_overlap
     - name: batch_integration/metrics/graph_connectivity
     - name: batch_integration/metrics/hvg_overlap

diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf
@@ -37,7 +37,7 @@ workflow run_wf {
   metrics = [
     asw_batch,
     asw_label,
-    // cell_cycle_conservation,
+    cell_cycle_conservation,
     clustering_overlap,
     graph_connectivity,
     hvg_overlap,