adds gc calc and reporting #107
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| name: fastq-peek functional test # Name of the workflow | |
| on: | |
| pull_request: | |
| branches: | |
| - main # Trigger the workflow on pull requests to the main branch | |
| jobs: # Define jobs for the workflow | |
| verify-fqp-output: # Job name | |
| runs-on: ubuntu-latest # Specify the environment to run the job | |
| steps: # Steps to execute in the job | |
| - name: Checkout code # Step to checkout the repository code | |
| uses: actions/checkout@v2 # Use the checkout action | |
| - name: Make script executable # Step to make the script executable | |
| run: chmod +x ./bin/fastq-peek.sh # Change permissions to make the script executable | |
| - name: Run fastq-peek script # Step to run the script | |
| id: run_script # ID for referencing this step | |
| run: ./bin/fastq-peek.sh ./data/sample.fastq # Command to run the script with the sample FASTQ file | |
| - name: Verify output # Step to verify the output | |
| run: | | |
| # Save the expected output to a file | |
| echo "Processing FASTQ file: ./data/sample.fastq" > expected_output.txt | |
| echo "Number of reads in ./data/sample.fastq: 2" >> expected_output.txt | |
| echo "GC Content of reads in ./data/sample.fastq: 50%" >> expected_output.txt | |
| # Capture the actual output of the script and save it to a file | |
| ./bin/fastq-peek.sh ./data/sample.fastq > actual_output.txt | |
| # Print expected and actual outputs for debugging | |
| echo "Expected Output:" | |
| cat expected_output.txt | |
| echo "Actual Output:" | |
| cat actual_output.txt | |
| # Compare actual output with expected output | |
| if ! diff -q expected_output.txt actual_output.txt; then | |
| echo "Output did not match expected result." | |
| diff expected_output.txt actual_output.txt | |
| exit 1 | |
| fi | |
| shell: bash |