Adapted contamination estimation workflow and BAMutils workflow for s…

[shadizaheri]

Summary of Changes

Updated the BAMUtil and LongRead ContaminationEstimation workflows from the PMICP branch to support short-read contamination analysis. The following modifications were made:

1. BAMUtil Adjustments:

• Modified the BAMutils.wdl on PMICP_main branch.
  • Adapted genotyping site references to use short-read specific BED files.
  • Updated thresholds for BAM size and coverage based on short-read data characteristics.
  • Adjusted parameters such as disk_type, max_retries, and runtime resource allocations to reflect the smaller file sizes and higher throughput of short-read data.

3. LongRead ContaminationEstimation Workflow:

• Modified the LongReadsContaminationEstimation.wdl on PMICP_main branch.
  • Renamed workflow and relevant components for short-read compatibility.
  • Updated reference files and options to match the requirements of short-read contamination estimation.
  • Tuned pileup generation parameters for better performance with short-read BAM files.

Next, I will test these changes on Terra to ensure compatibility with short-read datasets.