Add GATK contamination check for WES/WGS samples

[dorotejavujinovic]

Description

Adds GATK-based contamination detection to complement VerifyBamID2 for more reliable contamination estimation across both WGS and WES samples.

Motivation

• VerifyBamID2 works well for WGS but has significant limitations with WES data
• GATK CalculateContamination performs better on targeted sequencing (WES)
• Having both methods for WGS provides cross-validation and increases confidence

Changes

• Add CONTAMINATION_CHECK subworkflow using GATK4
• Add PARSE_CONTAMINATION module for MultiQC integration
• Add GATK4 GetPileupSummaries and CalculateContamination modules
• Implement conditional intervals handling (WGS vs WES)
• Configure MultiQC to display contamination results with thresholds

Usage

params.run_contamination = true
params.contamination_sites = "/path/to/small_exac_common_3.hg38.vcf.gz"
params.contamination_sites_tbi = "/path/to/small_exac_common_3.hg38.vcf.gz.tbi"

Testing

• Tested on WGS samples
• Tested on WES samples
• MultiQC integration verified

Technical Details

• WGS: Uses Channel.empty() for genome-wide analysis
• WES: Uses target BED file for exome-restricted analysis
• Results displayed in MultiQC with color-coded contamination thresholds (<2% green, 2-5% yellow, >5% red)