Feature request: Add Subcommands for Specific Steps

[berntpopp]

Description: Add subcommands for generating only exclusion or inclusion BED files without running the full pipeline. Possible subcommands:

• generate-exclusion-bed
• generate-inclusion-bed
• run-pipeline

[berntpopp]

Plan for Subcommands Implementation in Bash Script

Objective:

To implement three subcommands:

1. generate-exclusion-bed: Generates exclusion BED files only.
2. generate-inclusion-bed: Generates inclusion BED files only.
3. run-pipeline: Executes the entire pipeline, including BED file generation, VCF normalization, annotation, and filtering.

Implementation Plan:

1. Subcommands:

   • Use a case block to parse and execute specific subcommands based on user input.

2. Functions:

   • generate_exclusion_bed():
     • Normalize exclusion BED files.
     • Combine and process the BED files.
     • Compress and index the output files.
   • generate_inclusion_bed():
     • Normalize inclusion BED files.
     • Combine and process the BED files.
     • Compress and index the output files.
   • run_pipeline():
     • Call both generate_exclusion_bed() and generate_inclusion_bed().
     • Normalize the VCF using bcftools norm.
     • Annotate the VCF using the generated BED files with bcftools annotate.
     • Apply filters using bcftools filter.
     • Generate statistics and plots (optional).

3. Helper Functions:

   • normalize_bed(): Applies sorting and annotation to a BED file.
   • combine_and_process_bed(): Merges, compresses, and indexes the BED files.
   • normalize_and_annotate_vcf(): Handles VCF normalization and annotation using bcftools.

4. Execution Flow:

   • If the user runs generate-exclusion-bed, only the exclusion BED files will be generated.
   • If the user runs generate-inclusion-bed, only the inclusion BED files will be generated.
   • If the user runs run-pipeline, all steps are executed sequentially, including VCF processing.

5. Debugging and Logging:

   • Ensure all steps are logged with appropriate messages.
   • Use debug_msg() for detailed command logs when --debug is enabled.

6. Error Handling:

   • Apply consistent error handling using || { log_msg "Error"; exit 1; } after critical commands.

7. Testing:

   • Test each subcommand separately to ensure modular functionality.
   • Test run-pipeline to confirm the full workflow is executed correctly.