Add Padfoot annotation and ReConPlot figures for the SV/CNA callers - #202

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Tim-Yu wants to merge 10 commits into

IntGenomicsLab:devfrom

Tim-Yu:feat/padfoot-reconplot-on-savana-pr189

Commits on Sep 23, 2026

Expose SAVANA BEDPE, purity/ploidy and allele counts for downstream annotation

authored and
Boyu YU
committed
5e0f888
Add Padfoot annotation and ReConPlot figures on top of the SAVANA subworkflows

authored and
Boyu YU
committed
95b1e17
Document Padfoot and ReConPlot across README, CITATIONS, CHANGELOG and docs

authored and
Boyu YU
committed
5bc9dc5
Move the Padfoot and ReConPlot wiring into local subworkflows

authored and
Boyu YU
committed
e667aae
Ship the ReConPlot wrapper under assets/ instead of downloading it at run time

authored and
Boyu YU
committed
5bbcc20
Name ReConPlot caller-pair folders SV caller first, matching Padfoot

authored and
Boyu YU
committed
e19467d
Add stub nf-tests for the Padfoot and ReConPlot subworkflows

authored and
Boyu YU
committed
931d2d1
Bring the Padfoot and ReConPlot docs in line with dev's conventions

authored and
Boyu YU
committed
edab7a2
Update usage instructions for VEP plugins

Tim-Yu
and
Copilot
authored
e793b61
Point the CHANGELOG entries at PR #202

Tim-Yu
authored and
Boyu YU
committed
8049f36