add process datasets test

src/workflows/process_datasets/test.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# Run this prior to executing this script:
+# bin/viash_build -q 'batch_integration'
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+set -e
+
+DATASETS_DIR="resources_test/common"
+OUTPUT_DIR="output/process_datasets_test"
+
+if [ ! -d "$OUTPUT_DIR" ]; then
+  mkdir -p "$OUTPUT_DIR"
+fi
+
+export NXF_VER=24.04.3
+
+nextflow run . \
+  -main-script target/nextflow/workflows/process_datasets/main.nf \
+  -profile docker \
+  -entry auto \
+  -c common/nextflow_helpers/labels_ci.config \
+  --id run_test \
+  --input_states "$DATASETS_DIR/**/state.yaml" \
+  --rename_keys 'input:output_dataset' \
+  --settings '{"output_train": "train.h5ad", "output_test": "test.h5ad"}' \
+  --publish_dir "$OUTPUT_DIR" \
+  --output_state "state.yaml"