Feat: Allow Input of Pre-Subset FASTQ Files into the Pipeline

[berntpopp]

• Description: The pipeline currently assumes input FASTQ files are full datasets. However, in some scenarios, users may want to input pre-subset FASTQ files, such as those generated from a range request of an online BAM file. The pipeline should be updated to handle these pre-subset FASTQ files as valid input without requiring further processing.
• Tasks:
  • Update the input handling logic to accept pre-subset FASTQ files.
  • Ensure that the pipeline can properly process these files without assuming they represent the entire dataset.
  • Document the changes and update the usage guide.

[berntpopp]

Relates to #45