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Add create_test_resources script
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#!/bin/bash | ||
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# get the root of the directory | ||
REPO_ROOT=$(git rev-parse --show-toplevel) | ||
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# ensure that the command below is run from the root of the repository | ||
cd "$REPO_ROOT" | ||
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set -e | ||
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RAW_DATA=resources_test/common | ||
DATASET_DIR=resources_test/task_template | ||
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mkdir -p $DATASET_DIR | ||
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# process dataset | ||
echo Running process_dataset | ||
nextflow run . \ | ||
-main-script target/nextflow/workflows/process_datasets/main.nf \ | ||
-profile docker \ | ||
-entry auto \ | ||
--input_states "$RAW_DATA/**/state.yaml" \ | ||
--rename_keys 'input:output_dataset' \ | ||
--settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' \ | ||
--publish_dir "$DATASET_DIR" \ | ||
--output_state '$id/state.yaml' | ||
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# run one method | ||
viash run src/methods/logistic_regression/config.vsh.yaml -- \ | ||
--input_train $DATASET_DIR/pancreas/train.h5ad \ | ||
--input_test $DATASET_DIR/pancreas/test.h5ad \ | ||
--output $DATASET_DIR/pancreas/denoised.h5ad | ||
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# run one metric | ||
viash run src/metrics/accuracy/config.vsh.yaml -- \ | ||
--input_predicition $DATASET_DIR/pancreas/predicted.h5ad \ | ||
--input_solution $DATASET_DIR/pancreas/solution.h5ad \ | ||
--output $DATASET_DIR/pancreas/score.h5ad |