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Increase subsample dimensions #392

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merged 3 commits into from
Mar 6, 2024
Merged

Increase subsample dimensions #392

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bbda1bb
Increase subsample dimensions
KaiWaldrant Feb 28, 2024
73d74e1
fix pancreas subsample error
KaiWaldrant Feb 29, 2024
4a72cb8
force CI
KaiWaldrant Mar 6, 2024
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3 changes: 3 additions & 0 deletions src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh
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Expand Up @@ -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'
Expand All @@ -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"

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4 changes: 3 additions & 1 deletion src/datasets/resource_test_scripts/pancreas.sh
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Expand Up @@ -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' \
Expand All @@ -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
1 change: 0 additions & 1 deletion src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml
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@@ -1,7 +1,6 @@
# use metric api spec
__merge__: ../../api/comp_metric_embedding.yaml
functionality:
status: disabled
name: cell_cycle_conservation
info:
metrics:
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2 changes: 1 addition & 1 deletion src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/tasks/batch_integration/workflows/run_benchmark/main.nf
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Expand Up @@ -37,7 +37,7 @@ workflow run_wf {
metrics = [
asw_batch,
asw_label,
// cell_cycle_conservation,
cell_cycle_conservation,
clustering_overlap,
graph_connectivity,
hvg_overlap,
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