Closed hyunhwan-bcm closed 1 month ago
Do you mean the default behavior is not performing the filtering? then it's good.
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?
Gotcha. I will work on it
Thanks!
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
--no_filter_exonic
to--exome_filter
--bed_filter
--bed_filter
over--exome_filter
Implementation Details
1. Rename parameter
--no_filter_exonic
to--exome_filter
--exome_filter
is true (instead of false)2. Add new parameter
--bed_filter
option3. Modify filtering logic
--bed_filter
is provided, use it for filtering regardless of--exome_filter
setting--bed_filter
is not provided, then check--exome_filter
FILTER_EXONIC
process to implement this logicCode Changes
Update the
FILTER_EXONIC
process (around line 53) to something like this:Tasks
--no_filter_exonic
to--exome_filter
throughout the codebase--bed_filter
parameter to the script