add to stdout

.github/workflows/test.yml

@@ -1,6 +1,6 @@
 name: CI
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   build:
@@ -24,7 +24,9 @@ jobs:
 
     - name: Verify output
       run: |
-        EXPECTED_OUTPUT="Processing FASTQ file: ./data/sample.fastq\nNumber of reads in ./data/sample.fastq: 2\nGC content in ./data/sample.fastq: 50%"
+        EXPECTED_OUTPUT="Processing FASTQ file: ./data/sample.fastq
+        Number of reads in ./data/sample.fastq: 2
+        GC content in ./data/sample.fastq: 50%"
         ACTUAL_OUTPUT=$(./bin/fastq-peak.sh ./data/sample.fastq)
         if [[ "$ACTUAL_OUTPUT" != "$EXPECTED_OUTPUT" ]]; then
           echo "Output did not match expected result."

bin/fastq-peak.sh

@@ -26,3 +26,13 @@ LINE_COUNT=$(wc -l < "$FASTQ_FILE")
 READ_COUNT=$((LINE_COUNT / 4))
 
 echo "Number of reads in $FASTQ_FILE: $READ_COUNT"
+
+# Calculate Percent GC
+## Count the number of G and C nucleotides
+GC_COUNT=$(grep -E '^[ATCGN]+$' "$FASTQ_FILE" | tr -cd 'GCgc' | wc -c)
+## Count the total number of nucleotides (A, T, C, G)
+TOTAL_BASE_COUNT=$(grep -E '^[ATCGN]+$' "$FASTQ_FILE" | tr -cd 'ATCGatcg' | wc -c)
+## Calculate the GC content as a percentage
+GC_CONTENT=$(awk "BEGIN {print ($GC_COUNT / $TOTAL_BASE_COUNT) * 100}")
+
+echo "GC content in $FASTQ_FILE: $GC_CONTENT%"