initial benchmark implementation

scripts/run_benchmark/run_test_local.sh

@@ -6,14 +6,6 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-# remove this when you have implemented the script
-echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
-echo "  Step 1: replace 'task_template' with the name of the task in the following command."
-echo "  Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
-echo "  Step 3: replace the settings parameter to fit your run_benchmark outputs"
-echo "  Step 4: remove this message"
-exit 1
-
 set -e
 
 echo "Running benchmark on test data"
@@ -28,9 +20,8 @@ nextflow run . \
   -profile docker \
   -resume \
   -c common/nextflow_helpers/labels_ci.config \
-  --id cxg_mouse_pancreas_atlas \
-  --input_train resources_test/task_template/cxg_mouse_pancreas_atlas/train.h5ad \
-  --input_test resources_test/task_template/cxg_mouse_pancreas_atlas/test.h5ad \
-  --input_solution resources_test/task_template/cxg_mouse_pancreas_atlas/solution.h5ad \
+  --id mouse_brain_combined \
+  --input_sc resources_test/task_ist_preprocessing/mouse_brain_combined/scrnaseq_reference.h5ad \
+  --input_sp resources_test/task_ist_preprocessing/mouse_brain_combined/raw_ist.zarr \
   --output_state state.yaml \
   --publish_dir "$publish_dir"

src/workflows/run_benchmark/config.vsh.yaml

@@ -42,12 +42,6 @@ argument_groups:
         required: true
         direction: output
         default: task_info.yaml
-  - name: Methods
-    arguments:
-      - name: "--method_ids"
-        type: string
-        multiple: true
-        description: A list of method ids to run. If not specified, all methods will be run.
 
 resources:
   - type: nextflow_script
@@ -57,13 +51,17 @@ resources:
     path: /_viash.yaml
 
 dependencies:
-  # - name: common/check_dataset_schema
-  #   repository: openproblems-v2
-  # - name: common/extract_metadata
-  #   repository: openproblems-v2
-  # - name: control_methods/true_labels
-  # - name: methods/logistic_regression
-  # - name: metrics/accuracy
+  - name: h5ad/extract_uns_metadata
+    repository: core
+  - name: methods_segmentation/custom_segmentation
+  - name: methods_transcript_assignment/basic_transcript_assignment
+  - name: methods_count_aggregation/basic_count_aggregation
+  - name: methods_qc_filter/basic_qc_filter
+  - name: methods_calculate_cell_volume/alpha_shapes
+  - name: methods_normalization/normalize_by_volume
+  - name: methods_cell_type_annotation/ssam
+  - name: methods_expression_correction/gene_efficiency_correction
+  - name: metrics/similarity
 
 runners:
   - type: nextflow