fix scripts and components

openproblems-bio · Sep 26, 2024 · 44f6171 · 44f6171
1 parent dc39223
commit 44f6171
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Showing 4 changed files with 11 additions and 6 deletions.
diff --git a/scripts/create_resources/process_allen_brain_cell_atlas_brain.sh b/scripts/create_resources/process_allen_brain_cell_atlas_brain.sh
@@ -8,7 +8,7 @@ cd "$REPO_ROOT"
 
 set -e
 
-publish_dir="s3://openproblems-data/resource/datasets"
+publish_dir="s3://openproblems-data/resources/datasets"
 
 cat > /tmp/params.yaml << HERE
 param_list:
@@ -53,3 +53,7 @@ tw launch https://github.com/openproblems-bio/task_ist_preprocessing.git \
   --params-file /tmp/params.yaml \
   --config common/nextflow_helpers/labels_tw.config \
   --labels datasets,allen_brain_cell_atlas
+
+aws s3 sync \
+  s3://openproblems-data/resources/datasets/allen_brain_cell_atlas/2023_yao_mouse_brain_scrnaseq_10xv2 \
+  resources/datasets/allen_brain_cell_atlas/2023_yao_mouse_brain_scrnaseq_10xv2
diff --git a/scripts/create_resources/process_datasets.sh b/scripts/create_resources/process_datasets.sh
@@ -37,6 +37,5 @@ tw launch https://github.com/openproblems-bio/task_ist_preprocessing.git \
   --workspace 53907369739130 \
   --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
   --params-file /tmp/params.yaml \
-  --entry-name auto \
   --config common/nextflow_helpers/labels_tw.config \
   --labels task_ist_preprocessing,process_datasets
diff --git a/scripts/create_test_resources/test_pipeline.sh b/scripts/create_test_resources/test_pipeline.sh
@@ -12,10 +12,10 @@ mkdir -p $OUT_DIR
 
 # run dataset preprocessor
 viash run src/data_processors/process_dataset/config.vsh.yaml -- \
-  --input_scrnaseq $SC_DIR/dataset.h5ad \
-  --input_ist $SP_DIR/dataset.zarr \
-  --output_scrnaseq $OUT_DIR/scrnaseq_reference.h5ad \
-  --output_ist $OUT_DIR/raw_ist.zarr
+  --input_sc $SC_DIR/dataset.h5ad \
+  --input_sp $SP_DIR/dataset.zarr \
+  --output_sc $OUT_DIR/scrnaseq_reference.h5ad \
+  --output_sp $OUT_DIR/raw_ist.zarr
 
 # run a segmentation method
 viash run src/methods_segmentation/custom_segmentation/config.vsh.yaml -- \

diff --git a/src/data_processors/process_dataset/config.vsh.yaml b/src/data_processors/process_dataset/config.vsh.yaml
@@ -17,3 +17,5 @@ engines:
 runners:
   - type: executable
   - type: nextflow
+    directives:
+      label: [lowcpu, highmem, hightime]