Add the option to generate complementary subgenic regions

[FerriolCalvet]

Update the add_hotspots.py script so that for each new subgenic region it also generates a new subgenic regions with the complementary part of the gene for the region, meaning a new region that contains all the positions of the gene except that specific domain/exon/subgenic region

• tested with domains, but not with exons

AI summary

This pull request adds support for generating complements of subgenic regions in the pipeline. The main changes introduce a new parameter, update configuration files, and modify the process to handle this new option.

Support for subgenic regions complement:

• Added a new boolean parameter omega_subgenic_regions_complement to nextflow.config to control whether complements for subgenic regions should be generated.
• Updated nextflow_schema.json to include documentation and UI metadata for the new omega_subgenic_regions_complement parameter.

Pipeline process updates:

• Modified the EXPAND_REGIONS process in modules/local/expand_regions/main.nf to pass the --subgenic-regions-complement flag to add_hotspots.py when the new parameter is enabled.

[Copilot]

Pull request overview

This pull request adds support for generating "negative" (complementary) regions for subgenic regions in the omega workflow. When enabled, for each subgenic region (domain/exon), the system will also create a region containing all positions of the gene except those in that specific subgenic region.

Key changes:

• Added new boolean parameter omega_negative_regions to control negative region generation
• Updated workflow to pass the --negative-regions flag when the parameter is enabled
• Implemented logic in add_hotspots.py to compute and output negative regions

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 1 comment.

File	Description
nextflow_schema.json	Documents the new omega_negative_regions parameter with description and help text
nextflow.config	Adds the omega_negative_regions parameter with default value of false
modules/local/expand_regions/main.nf	Passes the --negative-regions flag to the Python script based on the parameter value
bin/add_hotspots.py	Implements the core logic to generate negative regions by computing gene positions that exclude the subgenic region

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[FerriolCalvet]

This is how the result looks for some normal bladder test data:

TP53    all_samples     missense        71      8.981347656250017       0.0     6.9526096761226786      11.417260742187517
TP53    all_samples     truncating      9       7.606250000000015       5.6028366e-06   3.6180332946777414      13.941088867187517
TP53--P53       all_samples     missense        62      11.862500000000026      0.0     9.02452651977541        15.307324218750026
TP53--P53       all_samples     truncating      7       10.337500762939474      8.285046e-06    4.400952777992943       20.282569122314474
TP53--P53--negative     all_samples     missense        9       3.349609375000005       0.0026348233    1.6015325927734398      6.082763671875005
TP53--P53--negative     all_samples     truncating      2       4.532910156250008       0.08774614      0.7509357213974011      14.158154296875008
TP53--P53_TAD--negative all_samples     missense        70      8.836718750000017       0.0     6.828295440673841       11.250659179687517
TP53--P53_TAD--negative all_samples     truncating      9       7.9000000000000155      4.172325e-06    3.7546679687500073      14.469213867187516
TP53--P53_tetramer--negative    all_samples     missense        71      9.007812500000018       0.0     6.972540702819838       11.452270507812518
TP53--P53_tetramer--negative    all_samples     truncating      9       7.8687484741211104      4.2915344e-06   3.7417543413490133      14.425755310058612
TP53--TAD2      all_samples     missense        2       0.7246097564697264      0.6320096       0.12026205226778983     2.254761123657226
TP53--TAD2      all_samples     truncating      1       3.814059448242194       0.2758609       0.21524832472205196     17.552462768554694
TP53--TAD2--negative    all_samples     missense        69      13.087500000000027      0.0     10.097490539550803      16.684301757812527
TP53--TAD2--negative    all_samples     truncating      8       9.987304687500021       2.4437904e-06   4.521831691265115       18.86120605468752

[Copilot]

Pull request overview

Copilot reviewed 3 out of 4 changed files in this pull request and generated no new comments.

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