Execution workflows: Update execution workflows to output per-PAS fractional usage BED files

[SamBryce-Smith]

Relative usage implementation POC was done in #278

This is a Meta/Parent issue to keep track of tasks. We recently updated the execution workflow output specifications to report per-PAS relative usage in a BED file (#373). We need to update execution workflows for qualifying tools to output this information.

Currently the list is:

• DaPars - Execution workflow: DaPars - report Format 04 BED file in workflow (per-PAS fractional relative usage) #384
• DaPars2 - Execution workflow: DaPars2 - report Format 04 BED file in workflow (per-PAS fractional relative usage) #383 - PR execution workflow: DaPars2 - output Format 04 fractional relative usage quantification BED file #385
• QAPA - Execution workflow: QAPA - report Format 04 BED file in workflow (per-PAS fractional relative usage) #386
• Execution workflow: PAQR - report Format 04 BED file in workflow (per-PAS fractional relative usage) #387
• Execution workflow: APAtrap - report Format 04 BED file in workflow (per-PAS fractional relative usage) #416
• Execution workflow: TAPAS - report Format 04 BED file in workflow (per-PAS fractional relative usage) #426
• feat(Execution workflow): CSI-UTR - report Format 04 BED file in workflow (per-PAS fractional relative usage) #388
• Execution workflow: IsoSCM - report Format 04 BED file in workflow (per-PAS fractional relative usage) #389