From bbda1bbb0649a59eb8255bf0373b4077c0e72038 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 28 Feb 2024 16:44:18 +0100 Subject: [PATCH 1/3] Increase subsample dimensions MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com> --- src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh | 3 +++ src/datasets/resource_test_scripts/pancreas.sh | 2 ++ .../metrics/cell_cycle_conservation/config.vsh.yaml | 1 - .../batch_integration/workflows/run_benchmark/config.vsh.yaml | 2 +- src/tasks/batch_integration/workflows/run_benchmark/main.nf | 2 +- 5 files changed, 7 insertions(+), 3 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 index f6b5fc971c..3b5d35ee5c 100755 --- 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 index 9c0b1c5717..d576e405ec 100755 --- 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 1500 \ + --n_var 600 \ --output_raw '$id/raw.h5ad' \ --output_normalized '$id/normalized.h5ad' \ --output_hvg '$id/hvg.h5ad' \ 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 index cb1ef8bbae..78bae7b655 100644 --- 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 index 9525e736f5..b430734e22 100644 --- 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 index 91876737de..5543ac91cd 100644 --- 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, From 73d74e1329885a9d9358edc25b491b9a2adaf00b Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 29 Feb 2024 15:01:20 +0100 Subject: [PATCH 2/3] fix pancreas subsample error --- src/datasets/resource_test_scripts/pancreas.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index d576e405ec..4c6f0b0ae9 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -40,8 +40,8 @@ nextflow run . \ --seed 123 \ --normalization_methods log_cp10k \ --do_subsample true \ - --n_obs 1500 \ - --n_var 600 \ + --n_obs 600 \ + --n_var 1500 \ --output_raw '$id/raw.h5ad' \ --output_normalized '$id/normalized.h5ad' \ --output_hvg '$id/hvg.h5ad' \ @@ -58,4 +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 \ No newline at end of file From 4a72cb87d19e234f81e456d84d05ebcc6515f6be Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 6 Mar 2024 11:32:11 +0100 Subject: [PATCH 3/3] force CI