Large intermediate files in work/ directory, profiler setup challenges, and need for preprocessing skip option

[tarshad805]

Description of feature

Hi Muneeb,
First of all, thank you for providing such a powerful and well-designed pipeline.
Here are some issues I faced:

1. While running the pipeline, I noticed that large files such as aligned .bam and trimmed FASTQs appear in the work/ directory with their full sizes (GB-scale) duplicates existed in both work/ and results/ folders. This can quickly fill storage, especially for large sample sets.
2. Setting up the profiler took a lot of time and was challenging for me as a new user. More detailed guidance or examples for different environments (HPC, Conda, Docker) would make onboarding much easier please.
3. It would be very useful to have a parameter (e.g., --skip_preprocessing true) that allows skipping read trimming and QC steps for users who already have preprocessed reads.