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

Merged

ljwharbers merged 32 commits into

IntGenomicsLab:devfrom

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

Oct 7, 2026

Merged

Add Padfoot annotation and ReConPlot figures for the SV/CNA callers#202
ljwharbers merged 32 commits into
IntGenomicsLab:devfrom
Tim-Yu:feat/padfoot-reconplot-on-savana-pr189

Commits on Oct 2, 2026
- Expose SAVANA BEDPE, purity/ploidy and allele counts for downstream annotation
  
  Tim-Yu
  and
  claude
  committed
  382b4be
- Add Padfoot annotation and ReConPlot figures on top of the SAVANA subworkflows
  
  Tim-Yu
  and
  claude
  committed
  b0caeb0
- Document Padfoot and ReConPlot across README, CITATIONS, CHANGELOG and docs
  
  Tim-Yu
  and
  claude
  committed
  cad01d9
- Move the Padfoot and ReConPlot wiring into local subworkflows
  
  Tim-Yu
  and
  claude
  committed
  301bcb8
- Ship the ReConPlot wrapper under assets/ instead of downloading it at run time
  
  Tim-Yu
  and
  claude
  committed
  db09218
- Name ReConPlot caller-pair folders SV caller first, matching Padfoot
  
  Tim-Yu
  and
  claude
  committed
  5fd3ef2
- Add stub nf-tests for the Padfoot and ReConPlot subworkflows
  
  Tim-Yu
  and
  claude
  committed
  dd2e5c0
- Bring the Padfoot and ReConPlot docs in line with dev's conventions
  
  Tim-Yu
  and
  claude
  committed
  bc0ff52
- Update usage instructions for VEP plugins
  
  Tim-Yu
  and
  Copilot
  committed
  bd858a5
- Point the CHANGELOG entries at PR #202
  Tim-Yu
  committed
  8ba81b4
- Ship Padfoot and the ReConPlot package inside their images, drop the run-time downloads
  
  Tim-Yu
  and
  claude
  committed
  d29b27a
- Assert on the files each stub task receives, and cover ASCAT + Severus for tumour-only samples
  
  Tim-Yu
  and
  claude
  committed
  f0e9b67
- Make the two known ReConPlot failure modes warn-and-continue, validate --reconplot_regions at start-up
  
  Tim-Yu
  and
  claude
  committed
  5332502
- Share the Padfoot genome gate between the workflow and the parameter validator
  
  Tim-Yu
  and
  claude
  committed
  d42f18f
- Restore the second collapsed admonition in docs/usage.md and realign the option tables
  
  Tim-Yu
  and
  claude
  committed
  bdc3b72
- Drop the Go-template example from the Padfoot container README
  
  Tim-Yu
  and
  claude
  committed
  f04d3b8
- Address the automated review: run the module tests in PR CI, add help_text to every new parameter, fix two doc leftovers
  
  Tim-Yu
  and
  claude
  committed
  26e2c32
- Use the singularity/docker container ternary for PADFOOT and RECONPLOT with prebuilt SIF twins
  
  Tim-Yu
  and
  claude
  committed
  5b87b18
- Run PADFOOT and RECONPLOT for real in CI on synthetic fixtures
  
  Tim-Yu
  and
  claude
  committed
  962c3f5
- Harden the ReConPlot wrapper: stable tables, no aborts on odd records, consistent filters
  
  Tim-Yu
  and
  claude
  committed
  d2dc551
- Guard the Padfoot/ReConPlot configuration: species name, quoting, validation, skip under conda
  
  Tim-Yu
  and
  claude
  committed
  fd878b3
- Move the Padfoot and ReConPlot images to Docker Hub, fix the ReConPlot genome-wide clipping, label copy number against the tumour ploidy
  
  Tim-Yu
  and
  claude
  committed
  57c5af0
- Docs and metadata follow-ups from the review
  
  Tim-Yu
  and
  claude
  committed
  4536872
Commits on Oct 5, 2026
Commits on Oct 7, 2026
- Draw SAVANA ReConPlot figures for PacBio samples from the somatic VCF
  
  ljwharbers
  and
  claude
  committed
  5453919

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

Add Padfoot annotation and ReConPlot figures for the SV/CNA callers#202
ljwharbers merged 32 commits into
IntGenomicsLab:devfrom
Tim-Yu:feat/padfoot-reconplot-on-savana-pr189

Commits on Oct 2, 2026

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

Add Padfoot annotation and ReConPlot figures on top of the SAVANA subworkflows

Document Padfoot and ReConPlot across README, CITATIONS, CHANGELOG and docs

Move the Padfoot and ReConPlot wiring into local subworkflows

Ship the ReConPlot wrapper under assets/ instead of downloading it at run time

Name ReConPlot caller-pair folders SV caller first, matching Padfoot

Add stub nf-tests for the Padfoot and ReConPlot subworkflows

Bring the Padfoot and ReConPlot docs in line with dev's conventions

Update usage instructions for VEP plugins

Point the CHANGELOG entries at PR #202

Ship Padfoot and the ReConPlot package inside their images, drop the run-time downloads

Assert on the files each stub task receives, and cover ASCAT + Severus for tumour-only samples

Make the two known ReConPlot failure modes warn-and-continue, validate --reconplot_regions at start-up

Share the Padfoot genome gate between the workflow and the parameter validator

Restore the second collapsed admonition in docs/usage.md and realign the option tables

Drop the Go-template example from the Padfoot container README

Address the automated review: run the module tests in PR CI, add help_text to every new parameter, fix two doc leftovers

Use the singularity/docker container ternary for PADFOOT and RECONPLOT with prebuilt SIF twins

Run PADFOOT and RECONPLOT for real in CI on synthetic fixtures

Harden the ReConPlot wrapper: stable tables, no aborts on odd records, consistent filters

Guard the Padfoot/ReConPlot configuration: species name, quoting, validation, skip under conda

Move the Padfoot and ReConPlot images to Docker Hub, fix the ReConPlot genome-wide clipping, label copy number against the tumour ploidy

Docs and metadata follow-ups from the review

Commits on Oct 5, 2026

Use Padfoot 3846215: correct breakpoint-to-gene lookup, exon/intron labels and known-fusion detection

Keep the ReConPlot figures a task could draw, and skip ASCAT pairs without a solution

Read Wakhan 0.5.0's ranked solutions in Padfoot and ReConPlot

Retry resource kills before ignoring, fix the mm10 species, keep SAVANA figures without SVs, check --padfoot_genome

Use Padfoot 1748e84: custom annotations, quoted commands, breakpoint repeats, robust Wakhan input

Act on the second independent review: valid stub versions, Dfam outside /home, non-fatal focus panel, cache and gate fixes

Check the Padfoot and ReConPlot steps in the preview test's workflow graph

Satisfy pre-commit and nf-core lint for the new fixtures and preview test

Commits on Oct 7, 2026

Draw SAVANA ReConPlot figures for PacBio samples from the somatic VCF