diff --git a/scripts/create_resources/process_allen_brain_cell_atlas_brain.sh b/scripts/create_resources/process_allen_brain_cell_atlas_brain.sh index 891ebe8a..3aa72bf4 100755 --- 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 index e4852017..4c3476a2 100755 --- 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 index 63810a71..12a700e9 100755 --- 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 index 836b0e22..e53e7f6b 100644 --- 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] \ No newline at end of file