Test script

src/nanoplot/test.sh

@@ -3,19 +3,212 @@
 set -e
 
 ## VIASH START
-meta_executable="$PWD/target/executable/NanoPlot/NanoPlot"
+meta_executable="$PWD/target/executable/nanoplot/nanoplot"
 meta_resources_dir="$PWD/src/nanoplot"
 ## VIASH END
 
-echo "> Run NanoPlot"
+###########################################################################
+
+# Test 1: Run NanoPlot with only input parameter
+
+echo "> Run Test 1: one input"
 "$meta_executable" \
-  --fastq "$meta_resources_dir/test_data/real.fastq" \
-  -o "output"
+  --fastq "$meta_resources_dir/test_data/test1.fastq"
 
-echo ">> Check if output directory is empty"
-if [ -z "$(ls -A ./output)" ]; then
-    echo "No output"
-    exit 1
+# Check if HTML file is generated
+if ! ls target/result/*.html 1> /dev/null 2>&1; then
+  echo "Output HTML file not found"
+  exit 1
+fi
+
+# Check if summary file is generated
+if ! ls target/result/*.txt 1> /dev/null 2>&1; then
+  echo "NanoPlot summary file not found"
+  exit 1
+fi
+
+# Check if plots are generated
+if ! ls target/result/*.png 1> /dev/null 2>&1; then
+  echo "Plots are not found"
+  exit 1
+fi
+
+# Check if files are empty
+if find target/result -name "*.html" -type f -size 0 | grep -q .; then 
+  echo "At least one HTML file is empty."
+  exit 1
+fi
+if find target/result -name "*.png" -type f -size 0 | grep -q .; then 
+  echo "At least one plot is empty."
+  exit 1
 fi
+if find target/result -name "*.txt" -type f -size 0 | grep -q .; then 
+  echo "NanoPlot summary file is empty."
+  exit 1
+fi
+
+# rm -f target/result/* # Clear output
+
+echo "Test 1 succeeded."
+
+###########################################################################
+
+# Test 2: Run NanoPlot with multiple inputs
+
+echo "> Run Test 2: multiple inputs"
+"$meta_executable" \
+  --fastq "$meta_resources_dir/test_data/test1.fastq" "$meta_resources_dir/test_data/test2.fastq"
+
+# Check if HTML file is generated
+if ! ls target/result/*.html 1> /dev/null 2>&1; then
+  echo "Output HTML file not found"
+  exit 1
+fi
+
+# Check if summary file is generated
+if ! ls target/result/*.txt 1> /dev/null 2>&1; then
+  echo "NanoPlot summary file not found"
+  exit 1
+fi
+
+# Check if plots are generated
+if ! ls target/result/*.png 1> /dev/null 2>&1; then
+  echo "Plots are not found"
+  exit 1
+fi
+
+# Check if files are empty
+if find target/result -name "*.html" -type f -size 0 | grep -q .; then 
+  echo "At least one HTML file is empty."
+  exit 1
+fi
+if find target/result -name "*.png" -type f -size 0 | grep -q .; then 
+  echo "At least one plot is empty."
+  exit 1
+fi
+if find target/result -name "*.txt" -type f -size 0 | grep -q .; then 
+  echo "NanoPlot summary file is empty."
+  exit 1
+fi
+
+# rm -f target/result/* # Clear output
+
+echo "Test 2 succeeded."
+
+###########################################################################
+
+# Test 3: Run NanoPlot with multiple options
+
+echo "> Run Test 3: multiple options"
+"$meta_executable" \
+  --fastq "$meta_resources_dir/test_data/test1.fastq" \
+  -t 2 \
+  --maxlength 40000 \
+  --format jpg \
+  --prefix biobox_ \
+  --store \
+  --color yellow \
+  --info_in_report
+
+# Check if HTML file is generated
+if ! ls target/result/*.html 1> /dev/null 2>&1; then
+  echo "Output HTML file not found"
+  exit 1
+fi
+
+# Check if summary file is generated
+if ! ls target/result/*.txt 1> /dev/null 2>&1; then
+  echo "NanoPlot summary file not found"
+  exit 1
+fi
+
+# Check if plots are generated (.jpg)
+if ! ls target/result/*.jpg 1> /dev/null 2>&1; then
+  echo "Plots are not found"
+  exit 1
+fi
+
+# Check if the extracted data exists (--store)
+if ! ls target/result/*.pickle 1> /dev/null 2>&1; then
+  echo "Extracted data are not found"
+  exit 1
+fi
+
+# Check if files are empty
+if find target/result -name "*.html" -type f -size 0 | grep -q .; then 
+  echo "At least one HTML file is empty."
+  exit 1
+fi
+if find target/result -name "*.jpg" -type f -size 0 | grep -q .; then 
+  echo "At least one plot is empty."
+  exit 1
+fi
+if find target/result -name "*.txt" -type f -size 0 | grep -q .; then 
+  echo "NanoPlot summary file is empty."
+  exit 1
+fi
+if find target/result -name "*.pickle" -type f -size 0 | grep -q .; then 
+  echo "Extracted data is empty."
+  exit 1
+fi
+
+# Check if the output file starts with "biobox" prefic
+if ! ls target/result/biobox* 1> /dev/null 2>&1; then
+    echo "The prefix is not added to the output files."
+else
+
+# rm -f target/result/* # Clear output
+
+echo "Test 3 succeeded."
+
+###########################################################################
+
+# Test 4: Run NanoPlot with output options
+
+echo "> Run Test 4: output options"
+"$meta_executable" \
+  --fastq "$meta_resources_dir/test_data/test1.fastq" \
+  --html "out/*.html" \
+  --log "out/*.log" \
+  --statsum "out/*.txt"
+
+# Check if HTML file is generated
+if ! ls out/*.html 1> /dev/null 2>&1; then
+  echo "Output HTML file not found"
+  exit 1
+fi
+
+# Check if summary file is generated
+if ! ls out/*.txt 1> /dev/null 2>&1; then
+  echo "NanoPlot summary file not found"
+  exit 1
+fi
+
+# Check if plots are generated (.jpg)
+if ! ls target/result/*.png 1> /dev/null 2>&1; then
+  echo "Plots are not found"
+  exit 1
+fi
+
+# Check if files are empty
+if find out -name "*.html" -type f -size 0 | grep -q .; then 
+  echo "At least one HTML file is empty."
+  exit 1
+fi
+if find target/result -name "*.png" -type f -size 0 | grep -q .; then 
+  echo "At least one plot is empty."
+  exit 1
+fi
+if find out -name "*.txt" -type f -size 0 | grep -q .; then 
+  echo "NanoPlot summary file is empty."
+  exit 1
+fi
+
+# rm -f target/result/* # Clear output
+# rm -rf out/ # Delete user-defined directory
+
+echo "Test 4 succeeded."
+
+###########################################################################
 
-# Check whether the contents of the resulting file is correct
+echo "All tests successfully completed!"

src/nanoplot/test_data/script.sh

@@ -55,6 +55,8 @@ for i in $(seq 1 $NUM_READS); do
     echo >> $OUTPUT_FILE  # Add a blank line between reads
 done
 
+#########################################################################################
+
 ## Bam file ##
 if [ ! -d /tmp/snakemake-wrappers ]; then
   git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers