Fixing critical typo in HaplotypeCaller disk spec.

[jonn-smith]

No description provided.

[shadizaheri]

Thank you for the great work on these updates. I tested this branch on 3,000 malaria samples with the SRFlowcell workflow on Terra and it worked perfectly.
Based on my observations, I’ve written a summary of the changes. Please correct any parts if needed. This summary is meant to clearly summarize the updates in this PR for both users and developers.

Review Summary of Key Improvements

1. Refactoring the Output Calculation Logic:

   • This PR simplifies complex calculation expressions by breaking them into smaller, clearly defined variables. It also prevents errors by incorporating conditional checks to handle cases like division by zero.
   • Metrics such as estimated fold coverage and aligned fraction of bases are now calculated upfront and stored in descriptive variables, which are then used in the output block. This approach improves the readability of the code and centralizes the logic for easier future adjustments.

2. Enhanced Error Handling in QC Tasks:

   • The PR also addresses the error handling in the FastQC QC tasks. By adding checks to ensure that base quality data is present before proceeding with calculations, the workflow is made more robust against incomplete data, which could lead to runtime errors.

3. Optimization of Java Options in Utility Tasks

4. HaplotypeCaller wdl Change in Source for gVCF Files:

   • The output_gvcf and output_gvcf_index are now sourced from ReblockHcGVCF.output_gvcf and ReblockHcGVCF.output_gvcf_index, respectively.
   • Previously, these files were sourced from MergeGVCFs.output_vcf and MergeGVCFs.output_vcf_index, indicating that the gVCF files were directly obtained from the merging of multiple GVCF files without additional processing.

[shadizaheri]

Please check the conversation for the details.