Add CRAM to FASTQ WDL to resolve STAR alignment hang issues

[shadizaheri]

This PR adds a WDL workflow to convert CRAM files to gzipped FASTQs via aligned BAM and uBAM intermediates.

Purpose: This was built to resolve STAR alignment hangs caused by problematic reads near the end of FASTQ files during multithreaded runs. Re-generating FASTQs via Picard’s RevertSam and SamToFastq successfully resolved the issue across STAR versions v2.5.3a, v2.7.10a, and v2.7.11b.

Workflow Steps

1. CRAM → BAM using samtools view
2. BAM → uBAM using GATK RevertSam
3. uBAM → FASTQ using GATK SamToFastq

Outputs

• _1.fastq.gz
• _2.fastq.gz
• _unpaired.fastq.gz

The wdl has been tested throughout the pipeline and mitigates STAR alignment failures caused by problematic reads accumulating at the end of FASTQ files during multithreaded alignment.