Added more tests

src/fastqc/config.vsh.yaml

@@ -35,7 +35,6 @@ argument_groups:
       - name: --zip
         type: file
         direction: output
-        multiple: true
         multiple_sep: ","
         description: |
           Create the zip file(s) containing: html report, data, images, icons etc.

src/fastqc/script.sh

@@ -36,41 +36,44 @@ fastqc \
   ${par_dir:+--dir "$par_dir"} \
   ${par_input:+ ${input[*]}}
 
-# input_dir=$(dirname ${input[1]})
-# # Both outputs args passed
-# if [[ -n "$par_html" ]] && [[ -n "$par_zip" ]]; then
-#   IFS=',' read -r -a html_files <<< "$par_html"
-#   IFS=',' read -r -a zip_files <<< "$par_zip"
-#   for i in "${!input[@]}"; do
-#     sample_name=$(basename ${input[$i]} .fq)
-#     input_zip="$input_dir/${sample_name}_fastqc.zip"
-#     input_html="$input_dir/${sample_name}_fastqc.html"
-#     zip_file=${zip_files[$i]}
-#     html_file=${html_files[$i]}
-#     mv "$input_zip" "$zip_file"
-#     mv "$input_html" "$html_file"
-#   done
-# # Only html output arg passed
-# elif [[ -n "$par_html" ]]; then
-#   IFS=',' read -r -a html_files <<< "$par_html"
-#   for i in "${!input[@]}"; do
-#     sample_name=$(basename ${input[$i]} .fq)
-#     input_html="$input_dir/${sample_name}_fastqc.html"
-#     html_file=${html_files[$i]}
-#     mv "$input_html" "$html_file"
-#   done
-#   rm "$input_dir"/*.zip
-# # Only zip output arg passed
-# elif [[ -n "$par_zip" ]]; then
-#   IFS=',' read -r -a zip_files <<< "$par_zip"
-#   for i in "${!input[@]}"; do
-#     sample_name=$(basename ${input[$i]} .fq)
-#     input_zip="$input_dir/${sample_name}_fastqc.zip"
-#     zip_file=${zip_files[$i]}
-#     mv "$input_zip" "$zip_file"
-#   done
-#   rm "$input_dir"/*.html
-# fi
+input_dir=$(dirname ${input[0]})
+# echo "input dir: $input_dir"
+# echo "input: ${input[*]}"
+
+# Both outputs args passed
+if [[ -n "$par_html" ]] && [[ -n "$par_zip" ]]; then
+  IFS=',' read -r -a html_files <<< "$par_html"
+  IFS=',' read -r -a zip_files <<< "$par_zip"
+  for i in "${!input[@]}"; do
+    sample_name=$(basename ${input[$i]} .fq)
+    input_zip="$input_dir/${sample_name}_fastqc.zip"
+    input_html="$input_dir/${sample_name}_fastqc.html"
+    zip_file=${zip_files[$i]}
+    html_file=${html_files[$i]}
+    mv "$input_zip" "$zip_file"
+    mv "$input_html" "$html_file"
+  done
+# Only html output arg passed
+elif [[ -n "$par_html" ]]; then
+  IFS=',' read -r -a html_files <<< "$par_html"
+  for i in "${!input[@]}"; do
+    sample_name=$(basename ${input[$i]} .fq)
+    input_html="$input_dir/${sample_name}_fastqc.html"
+    html_file=${html_files[$i]}
+    mv "$input_html" "$html_file"
+  done
+  rm "$input_dir"/*.zip
+# Only zip output arg passed
+elif [[ -n "$par_zip" ]]; then
+  IFS=',' read -r -a zip_files <<< "$par_zip"
+  for i in "${!input[@]}"; do
+    sample_name=$(basename ${input[$i]} .fq)
+    input_zip="$input_dir/${sample_name}_fastqc.zip"
+    zip_file=${zip_files[$i]}
+    mv "$input_zip" "$zip_file"
+  done
+  rm "$input_dir"/*.html
+fi
 
 
 # Questions:

src/fastqc/test.sh

@@ -27,6 +27,19 @@ CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNNNNNNANNNCGAGGCCCTGGGGTAGAGGGNN
 @?@DDDDDDHHH?GH:?FCBGGB@C?DBEGIIIIAEF;FCGGI#########################################################
 EOL
 
+# Create and populate contaminants.txt
+printf "contaminant_sequence1\tCACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGA\n" > "test_data/contaminants.txt"
+printf "contaminant_sequence2\tGATCTTGG\n" >> "test_data/contaminants.txt"
+
+# Create and populate SAM file 
+printf "@HD\tVN:1.0\tSO:unsorted\n" > "test_data/example.sam"
+printf "@SQ\tSN:chr1\tLN:248956422\n" >> "test_data/example.sam"
+printf "@SQ\tSN:chr2\tLN:242193529\n" >> "test_data/example.sam"
+printf "@PG\tID:bowtie2\tPN:bowtie2\tVN:2.3.4.1\tCL:\"/usr/bin/bowtie2-align-s --wrapper basic-0 -x genome -U reads.fq -S output.sam\"\n" >> "test_data/example.sam"
+printf "read1\t0\tchr1\t100\t255\t50M\t*\t0\t0\tACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-10\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n" >> "test_data/example.sam"
+printf "read2\t0\tchr2\t150\t255\t50M\t*\t0\t0\tTGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-8\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n" >> "test_data/example.sam"
+printf "read3\t16\tchr1\t200\t255\t50M\t*\t0\t0\tGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU" >> "test_data/example.sam"
+
 cat > "test_data/expected_summary.txt" <<EOL
 PASS	Basic Statistics	input_1.fq
 PASS	Per base sequence quality	input_1.fq
@@ -53,79 +66,217 @@ FAIL	Overrepresented sequences	input_2.fq
 PASS	Adapter Content	input_2.fq
 EOL
 
+cat > "test_data/expected_summary_sam.txt" <<EOL
+PASS	Basic Statistics	example.sam
+PASS	Per base sequence quality	example.sam
+FAIL	Per sequence quality scores	example.sam
+FAIL	Per base sequence content	example.sam
+WARN	Per sequence GC content	example.sam
+PASS	Per base N content	example.sam
+WARN	Sequence Length Distribution	example.sam
+PASS	Sequence Duplication Levels	example.sam
+FAIL	Overrepresented sequences	example.sam
+PASS	Adapter Content	example.sam
+EOL
+
 # Test 1: Run fastqc with default parameters
-mkdir test1
-cd test1
-echo "-> Run Test without options"
+echo "-> Run Test: one input"
 "$meta_executable" \
- --input "../test_data/input_1.fq" 
+ --extract \
+ --input "test_data/input_1.fq" 
 
 # Check if the html file was generated
-[ ! -f "../test_data/input_1_fastqc.html" ] \
+[ ! -f "test_data/input_1_fastqc.html" ] \
     && echo "Output HTML file not found." && exit 1
 
 # Check if the zip file was generated
-[ ! -f "../test_data/input_1_fastqc.zip" ] \
+[ ! -f "test_data/input_1_fastqc.zip" ] \
     && echo "Output ZIP file not found." && exit 1
 
 # Check if the files are empty
-[ ! -s "../test_data/input_1_fastqc.html" ] \
+[ ! -s "test_data/input_1_fastqc.html" ] \
     && echo "Output HTML file is empty." && exit 1
 
-[ ! -s "../test_data/input_1_fastqc.zip" ] \
+[ ! -s "test_data/input_1_fastqc.zip" ] \
     && echo "Output ZIP file is empty." && exit 1
 
-# Unzip the zip file
-unzip "../test_data/input_1_fastqc.zip" -d "../test_data/test1/"
-
 # Check if the summary.txt was extracted
-[ ! -f "../test_data/test1/input_1_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
+[ ! -f "test_data/input_1_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
 
 # Check if the summary.txt is correct
-diff -a "../test_data/expected_summary.txt" "../test_data/test1/input_1_fastqc/summary.txt" \
+diff -a "test_data/expected_summary.txt" "test_data/input_1_fastqc/summary.txt" \
     || (echo "Output summary file does not match expected output" && exit 1)
 
+rm -r "test_data/input_1_fastqc"
+rm "test_data/input_1_fastqc.html"
+rm "test_data/input_1_fastqc.zip"
+
 echo "- test succeeded -"
-cd ..
 
 # Test 2: Run fastqc with multiple inputs
-mkdir test2
-cd test2
-echo "-> Run Test with multiple inputs"
+echo "-> Run Test: two inputs"
 "$meta_executable" \
- --input "../test_data/input_1.fq,../test_data/input_2.fq"
+ --extract \
+ --input "test_data/input_1.fq,test_data/input_2.fq"
 
 # Check if the html files was generated
-[ ! -f "../test_data/input_1_fastqc.html" ] && [ ! -f "../test_data/input_2_fastqc.html" ] \
+[ ! -f "test_data/input_1_fastqc.html" ] && [ ! -f "test_data/input_2_fastqc.html" ] \
     && echo "Output HTML files not found." && exit 1
 
 # Check if the zip files was generated
-[ ! -f "../test_data/input_1_fastqc.zip" ] && [ ! -f "../test_data/input_2_fastqc.zip" ] \
+[ ! -f "test_data/input_1_fastqc.zip" ] && [ ! -f "test_data/input_2_fastqc.zip" ] \
     && echo "Output ZIP files not found." && exit 1
 
 # Check if the files are empty
-[ ! -s "../test_data/input_1_fastqc.html" ] && [ ! -s "../test_data/input_2_fastqc.html" ] \
+[ ! -s "test_data/input_1_fastqc.html" ] && [ ! -s "test_data/input_2_fastqc.html" ] \
     && echo "Output HTML files are empty." && exit 1
 
-[ ! -s "../test_data/input_1_fastqc.zip" ] && [ ! -s "../test_data/input_2_fastqc.zip" ] \
+[ ! -s "test_data/input_1_fastqc.zip" ] && [ ! -s "test_data/input_2_fastqc.zip" ] \
     && echo "Output ZIP files are empty." && exit 1
 
-# Unzip the zip files
-unzip "../test_data/input_1_fastqc.zip" -d "../test_data/test2/"
-unzip "../test_data/input_2_fastqc.zip" -d "../test_data/test2/"
+# Check if the summary.txt was extracted
+[ ! -f "test_data/input_1_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
+[ ! -f "test_data/input_2_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
+
+# Check if the summary.txt is correct
+diff -a "test_data/expected_summary.txt" "test_data/input_1_fastqc/summary.txt" \
+    || (echo "Output summary file does not match expected output" && exit 1)
+diff -a "test_data/expected_summary2.txt" "test_data/input_2_fastqc/summary.txt" \
+    || (echo "Output summary file does not match expected output" && exit 1)
+
+rm -r "test_data/input_1_fastqc"
+rm -r "test_data/input_2_fastqc"
+rm "test_data/input_1_fastqc.html"
+rm "test_data/input_2_fastqc.html"
+rm "test_data/input_1_fastqc.zip"
+rm "test_data/input_2_fastqc.zip"
+
+echo "- test succeeded -"
+
+# Test 3: Run fastqc with contaminants
+echo "-> Run Test: contaminants"
+"$meta_executable" \
+ --extract \
+ --input "test_data/input_1.fq" \
+ --contaminants "test_data/contaminants.txt"
+
+# Check if the html file was generated
+[ ! -f "test_data/input_1_fastqc.html" ] \
+    && echo "Output HTML file not found." && exit 1
+
+# Check if the zip file was generated
+[ ! -f "test_data/input_1_fastqc.zip" ] \
+    && echo "Output ZIP file not found." && exit 1
+
+# Check if the files are empty
+[ ! -s "test_data/input_1_fastqc.html" ] \
+    && echo "Output HTML file is empty." && exit 1
+
+[ ! -s "test_data/input_1_fastqc.zip" ] \
+    && echo "Output ZIP file is empty." && exit 1
+
+# Check if the summary.txt was extracted
+[ ! -f "test_data/input_1_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
+
+# Checking for contaminants in fastqc_data.txt
+echo "Checking for contaminants in fastqc_data.txt"
+result=$(cat test_data/input_1_fastqc/fastqc_data.txt | grep "contaminant" )
+expecte_result=$(printf "CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNN\t1\t100.0\tcontaminant_sequence1 (100%% over 44bp)\n")
+
+[ -z "$result" ] && echo "Contaminants not found in fastqc_data.txt" && exit 1
+
+[ "$result" != "$expecte_result" ] \
+ && echo "Contaminants do not match expected output" \
+ && echo "Result: $result" \
+ && echo "Expected: $expecte_result" \
+ && exit 1
+
+rm -r "test_data/input_1_fastqc"
+rm "test_data/input_1_fastqc.html"
+rm "test_data/input_1_fastqc.zip"
+
+echo "- test succeeded -"
+
+# Test 4: Run fastqc with sam file
+echo "-> Run Test: sam file"
+"$meta_executable" \
+ --extract \
+ --input "test_data/example.sam" \
+ --format "sam"
+
+# Check if the html file was generated
+[ ! -f "test_data/example_fastqc.html" ] \
+    && echo "Output HTML file not found." && exit 1
+
+# Check if the zip file was generated
+[ ! -f "test_data/example_fastqc.zip" ] \
+    && echo "Output ZIP file not found." && exit 1
+
+# Check if the files are empty
+[ ! -s "test_data/example_fastqc.html" ] \
+    && echo "Output HTML file is empty." && exit 1
+
+[ ! -s "test_data/example_fastqc.zip" ] \
+    && echo "Output ZIP file is empty." && exit 1
 
 # Check if the summary.txt was extracted
-[ ! -f "../test_data/test2/input_1_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
-[ ! -f "../test_data/test2/input_2_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
+[ ! -f "test_data/example_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
 
 # Check if the summary.txt is correct
-diff -a "../test_data/expected_summary.txt" "../test_data/test2/input_1_fastqc/summary.txt" \
+diff -a "test_data/expected_summary_sam.txt" "test_data/example_fastqc/summary.txt" \
     || (echo "Output summary file does not match expected output" && exit 1)
-diff -a "../test_data/expected_summary2.txt" "../test_data/test2/input_2_fastqc/summary.txt" \
+
+rm -r "test_data/example_fastqc"
+rm "test_data/example_fastqc.html"
+rm "test_data/example_fastqc.zip"
+
+echo "- test succeeded -"
+
+# Test 5: Run fastqc with multiple options
+echo "-> Run Test: multiple options"
+"$meta_executable" \
+ --extract \
+ --input "test_data/input_1.fq" \
+ --contaminants "test_data/contaminants.txt" \
+ --format "fastq" \
+ --casava \
+ --nofilter \
+ --nogroup \
+ --min_length 10 \
+ --threads 4 \
+ --kmers 5
+
+
+# Check if the html file was generated
+[ ! -f "test_data/input_1_fastqc.html" ] \
+    && echo "Output HTML file not found." && exit 1
+
+# Check if the zip file was generated
+[ ! -f "test_data/input_1_fastqc.zip" ] \
+    && echo "Output ZIP file not found." && exit 1
+
+# Check if the files are empty
+[ ! -s "test_data/input_1_fastqc.html" ] \
+    && echo "Output HTML file is empty." && exit 1
+
+[ ! -s "test_data/input_1_fastqc.zip" ] \
+    && echo "Output ZIP file is empty." && exit 1
+
+# Check if the summary.txt was extracted
+[ ! -f "test_data/input_1_fastqc/summary.txt" ] && echo "Extracted files not found." && exit 1
+
+# Check if the summary.txt is correct
+diff -a "test_data/expected_summary.txt" "test_data/input_1_fastqc/summary.txt" \
     || (echo "Output summary file does not match expected output" && exit 1)
 
+rm -r "test_data/input_1_fastqc"
+rm "test_data/input_1_fastqc.html"
+rm "test_data/input_1_fastqc.zip"
+
 echo "- test succeeded -"
-cd ..
+
+
+# Add more tests here
 
 echo "All tests succeeded!"
 exit 0

src/fastqc/test_data/contaminants.txt

@@ -0,0 +1,2 @@
+contaminant_sequence1	CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGA
+contaminant_sequence2	GATCTTGG

src/fastqc/test_data/example.sam

@@ -0,0 +1,7 @@
+@HD     VN:1.0  SO:unsorted
+@SQ     SN:chr1 LN:248956422
+@SQ     SN:chr2 LN:242193529
+@PG     ID:bowtie2     PN:bowtie2     VN:2.3.4.1  CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -x genome -U reads.fq -S output.sam"
+read1	0	chr1	100	255	50M	*	0	0	ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-10	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
+read2	0	chr2	150	255	50M	*	0	0	TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
+read3	16	chr1	200	255	50M	*	0	0	GCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU