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Update regressions code

Status: Open.

#287 In bbglab/deepCSA;

· FerriolCalvet opened on Apr 28, 2025

remove duplicated VEP subworkflow definition

Status: Open.

#302 In bbglab/deepCSA;

· FerriolCalvet opened on May 29, 2025

Plotting updates

Status: Open.

#308 In bbglab/deepCSA;

· FerriolCalvet opened on Jun 17, 2025

Use canonical colors for MutType plots

Status: Open.

#329 In bbglab/deepCSA;

· bkohrn opened on Jul 28, 2025

Documentation needed

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#139 In bbglab/deepCSA;

· FerriolCalvet opened on Aug 14, 2024

Revise that we are excluding MT DNA from the analysis

Status: Open.

Task

#220 In bbglab/deepCSA;

· FerriolCalvet opened on Jan 4, 2025

Adjust resource requirements of different processes to minimize burden for the cluster

Status: Open.

#262 In bbglab/deepCSA;

· FerriolCalvet opened on Mar 23, 2025

Define omega per sample QCs

Status: Open.

#318 In bbglab/deepCSA;

· FerriolCalvet opened on Jul 18, 2025

PLOTMETRICSQC

new-featureNew functionality being added.New functionality being added.

Status: Open.

#336 In bbglab/deepCSA;

· FerriolCalvet opened on Jul 31, 2025

Mutational profile stability

Status: Open.

#364 In bbglab/deepCSA;

· FerriolCalvet opened on Sep 11, 2025

Add ID signatures in sigprofilerAssignment

Status: Open.

#369 In bbglab/deepCSA;

· efigb opened on Sep 17, 2025

Fix bug in applyomegaqc plots

Status: Open.

Bug

#403 In bbglab/deepCSA;

· FerriolCalvet opened on Dec 19, 2025

add more mutation QCs

Status: Open.

#406 In bbglab/deepCSA;

· FerriolCalvet opened on Dec 21, 2025

add computation of mutation density at whole-genome level

Status: Open.

#398 In bbglab/deepCSA;

· FerriolCalvet opened on Dec 4, 2025

Test if it works with the duplexome

duplexome

Status: Open.

Task

#161 In bbglab/deepCSA;

· FerriolCalvet opened on Nov 15, 2024

Large memory usage by panel_postprocessing_annotation.py

Status: Open.

#407 In bbglab/deepCSA;

· scottrk opened on Dec 30, 2025

Dev chunk optimization postprocessveppanel

Status: Open (in progress).

bbglab/deepCSAnumber 390

#390 In bbglab/deepCSA;

· migrau opened on Nov 14, 2025

Define VAF distortion threshold from the nextflow.config

add-params

Status: Open.

Task

#233 In bbglab/deepCSA;

· FerriolCalvet opened on Jan 22, 2025

Explore discarding positions based on sequencing depth

Status: Open.

#410 In bbglab/deepCSA;

· m-huertasp opened on Jan 9, 2026

Run SigProfilerAssignment with the pipeline output of HDP

Status: Open.

#298 In bbglab/deepCSA;

· FerriolCalvet opened on May 14, 2025

use panel annotation to define already the protein position of each CDS position

Status: Open.

Task

#229 In bbglab/deepCSA;

· FerriolCalvet opened on Jan 15, 2025

SigProfilerExtractor

on-hold

Status: Open.

Feature

#236 In bbglab/deepCSA;

· FerriolCalvet opened on Jan 23, 2025

REFACTOR: Improve dna2protein bottleneck

code-review 👩‍💻Tasks associated with the code-reviewTasks associated with the code-review

efficiency-related

Status: Open (in progress).

bbglab/deepCSAnumber 422

#422 In bbglab/deepCSA;

· m-huertasp opened on Feb 24, 2026

Enhance the analysis of depths

enhancementNew feature or requestNew feature or request

HighHigh priorityHigh priority

Status: Open.

#145 In bbglab/deepCSA;

· FerriolCalvet opened on Sep 27, 2024

add decomposition of HDP with SigProfilerAssignment and minor fixes

Status: Draft (not ready).

bbglab/deepCSAnumber 425

#425 In bbglab/deepCSA;

· FerriolCalvet opened on Feb 26, 2026