Run the complete pipeline

[serpei]

Hi, thank you for your super-interesting tool.

I have some questions about the snakemake_config.yaml (If I plan to run all pipeline together using snakemake)

1. This file has to stay in the IRIS folder? So, if I want to run IRIS on multiple batches of patients I cannot do this in parallel?
2. If I want to run all steps to define the degree of association I only have to set run_all_modules at "true" and insert a list of normals in tissue_matched_normal_reference_group_names and tumors in tumor_reference_group_names?
3. Which are the differences between tissue_matched_normal_reference_group_names and normal_reference_group_names?
4. Can the user add its normal controls? And, if yes, how?
5. What's the meaning of "blocklist"?
6. What does mean comparison_mode "group" or "individual"?
7. For which kind of analyses you suggest stat_test_type parametric or non parametric?
8. Has sample_fastqs a maximum?
9. Are novel events considered automatically?
10. The parameter splice_event_type: has a user to run separately each event type?

Sorry to bother you, thank you, Serena