Modify exonic filtering parameters and add bed filter option

[hyunhwan-bcm]

Description

We need to make changes to the exonic filtering parameters in our Nextflow script to improve clarity and add more flexibility. This involves renaming an existing parameter and adding a new one with higher priority.

Proposed Changes

1. Rename --no_filter_exonic to --exome_filter
2. Add a new parameter --bed_filter
3. Modify the filtering logic to prioritize --bed_filter over --exome_filter

Implementation Details

1. Rename parameter

• Change --no_filter_exonic to --exome_filter
• Update the logic to check if --exome_filter is true (instead of false)

2. Add new parameter

• Add --bed_filter option
• This parameter should accept a path to a BED file for custom filtering

3. Modify filtering logic

• If --bed_filter is provided, use it for filtering regardless of --exome_filter setting
• If --bed_filter is not provided, then check --exome_filter
• Update the FILTER_EXONIC process to implement this logic

Code Changes

Update the FILTER_EXONIC process (around line 53) to something like this:

Tasks

• Rename --no_filter_exonic to --exome_filter throughout the codebase
• Add --bed_filter parameter to the script
• Update the `

[jylee-bcm]

Do you mean the default behavior is not performing the filtering? then it's good.

[hyunhwan-bcm]

please read the entire document carefully, this issue not only asking this but also add additional thing needs to be done. The current version the default parameter no_filter_exonic = false, then I believe it executes a filtering as default, isn't it?

[jylee-bcm]

Gotcha. I will work on it

[hyunhwan-bcm]

Thanks!