feat: add additional parameters and output processing steps to execut…

…e.sh

- Added new parameters (max_features, resolution, species, etc.) for R script execution.
- Updated output processing: included additional file types, created a zip archive, and moved final output.

service.cli/execute.sh

@@ -8,8 +8,8 @@ mkdir /home/scu/run
 cd /home/scu/run
 
 echo "starting service as"
-echo   User    : "$(id "$(whoami)")"
-echo   Workdir : "$(pwd)"
+echo "  User    : $(id "$(whoami)")"
+echo "  Workdir : $(pwd)"
 echo "..."
 echo
 
@@ -19,30 +19,48 @@ ls -al "${INPUT_FOLDER}"
 
 # Parse input parameters
 # Assuming these are passed as environment variables by osparc
-OUTPUT_PREFIX="${OUTPUT_PREFIX:-}"
+NAME="${NAME:-sPARcRNA}"
 MIN_CELLS="${MIN_CELLS:-3}"
 MIN_FEATURES="${MIN_FEATURES:-200}"
+MAX_FEATURES="${MAX_FEATURES:-2500}"
+RESOLUTION="${RESOLUTION:-0.8}"
+SPECIES="${SPECIES:-Homo sapiens}"
+MIN_PCT="${MIN_PCT:-0.25}"
+LOGFC_THRESHOLD="${LOGFC_THRESHOLD:-0.25}"
+GSEA_MIN_SIZE="${GSEA_MIN_SIZE:-15}"
+GSEA_MAX_SIZE="${GSEA_MAX_SIZE:-500}"
+CATEGORY="${CATEGORY:-H}"
 
 # Run the R script with command line arguments
 Rscript /home/${SC_USER_NAME}/dex.R \
   --input "$INPUT_FOLDER" \
   --output "$OUTPUT_FOLDER" \
-  --prefix "$OUTPUT_PREFIX" \
+  --name "$NAME" \
   --min_cells "$MIN_CELLS" \
-  --min_features "$MIN_FEATURES"
+  --min_features "$MIN_FEATURES" \
+  --max_features "$MAX_FEATURES" \
+  --resolution "$RESOLUTION" \
+  --species "$SPECIES" \
+  --min_pct "$MIN_PCT" \
+  --logfc_threshold "$LOGFC_THRESHOLD" \
+  --gsea_min_size "$GSEA_MIN_SIZE" \
+  --gsea_max_size "$GSEA_MAX_SIZE" \
+  --category "$CATEGORY"
 
 # Check if outputs.json was created
 if [ ! -f "${OUTPUT_FOLDER}/outputs.json" ]; then
     echo "Error: outputs.json was not created. Check R script execution."
     exit 1
 fi
 
+cp -r astro/ ./
+yarn build
+cp build/* "${OUTPUT_FOLDER}/"
+
 # Zip all output files
-cd "$OUTPUT_FOLDER"
-zip -r outputs.zip ./*.h5ad outputs.json
+zip -r outputs.zip "${OUTPUT_FOLDER}"/*.csv "${OUTPUT_FOLDER}"/*.png "${OUTPUT_FOLDER}"/*.rds "${OUTPUT_FOLDER}"/outputs.json
 
 # Move the zip file to be the only output
-mv outputs.zip final_output.zip
-rm ./*.h5ad outputs.json
+mv outputs.zip "${OUTPUT_FOLDER}/final_output.zip"
 
 echo "Service completed successfully."