Improvement: Add WDL Workflow for Automated IGV Screenshots with Customizable Resources and Inputs

[shadizaheri]

Overview
This PR introduces a new WDL workflow to automate the generation of IGV (Integrative Genomics Viewer) screenshots. The workflow allows users to input multiple BAM files, VCF files, and optional haplotype-specific alignments for visualization. Additionally, it includes options to customize memory, disk size, and snapshot height, ensuring flexibility for various use cases.

Key Features

• Multi-file Support: Handles multiple BAM files, including haplotypes (truth_haplotype_1, truth_haplotype_2, 8x-hap1, 8x-hap2), and a targeted VCF (TRGT_VCF) for comprehensive visualization.

• Customizable Resource Allocation: Users can specify memory, disk size, and image height to optimize the workflow for their dataset size and computational environment.

• Optional Inputs: Some inputs such as haplotype BAM files and VCF are optional, providing flexibility in the use of this workflow across different projects.

• Direct Screenshot Outputs: Outputs IGV screenshots directly as an array of PNG files, making it easy to review and download individual images.

Changes Included

• New WDL Workflow (IGVScreenshotWorkflow): A workflow to automate IGV screenshot generation using a Python script.

• Task (RunIGVScreenshot): A task that executes the IGV Python script within a Docker container, with support for a virtual display (Xvfb).

• Updated Documentation: Includes documentation in the WDL script header for easy understanding and usage.

Usage

1. Inputs: Users can provide the following inputs:

• BAM and BAI files (aligned_bam1, aligned_bam2)
• BED file for regions of interest
• Reference FASTA and FAI
• Optional haplotype BAMs (truth_haplotype_1, 8x-hap1, etc.)
• Optional targeted VCF and its index (TRGT_VCF, TRGT_VCF_tbi)
• Adjustable parameters: image_height, memory_mb, disk_gb

2. Execution: The workflow uses the provided inputs to generate IGV screenshots, saved as individual PNG files.
3. Output: The output is an array of screenshots directly accessible without compression.

How to Test

• Run the Workflow: Execute the WDL workflow on Terra or a WDL-compatible execution environment.

• Check Outputs: Verify that the screenshots are generated correctly in the specified output directory, and ensure optional files are handled as expected.

• Resource Customization: Test the workflow with different image_height, memory_mb, and disk_gb values to confirm customization works.

Potential Use Cases

• Visualizing genomic regions for multiple samples or haplotypes.
• Creating IGV snapshots for variant analysis and presentation.
• Generating high-resolution images for research publications.
  Additional Notes
  The Docker image used in this workflow is us.gcr.io/broad-dsp-lrma/igv_screenshot_docker:v9172024.
  This workflow is designed for flexibility and can be adapted to various genomic visualization needs.