feat(T2T): add initial implementation plan for T2T support

[johausmann]

No description provided.

[Copilot]

Pull request overview

This PR adds an initial technical implementation plan for supporting the T2T (CHM13v2.0) assembly in OBLX’s resource-pull and index-build Snakemake workflows.

Changes:

• Adds a step-by-step plan covering required config/schema updates for a T2T genome build.
• Outlines proposed new/modified pull rules for T2T-specific reference, annotation, variants, and masking resources (including a liftover path where needed).
• Lists required documentation and validation steps to integrate and dry-run the new build option.

Comments suppressed due to low confidence (3)

plans/T2T_implementation_plan.md:66

• Relative links in this section are also resolved from plans/, so they currently point to non-existent paths (e.g. plans/docs/...). Update link targets to be root-relative or prefixed with ../.

### A. [`docs/oblx/docs/configuration.md`](docs/oblx/docs/configuration.md)
- **Parameter List**: Update `genome_build` to include `T2T`.
- **Example Section**: Add a new "Example T2T" configuration block showing the use of `genome_build: T2T`.

### B. [`docs/oblx/docs/pull_resources.md`](docs/oblx/docs/pull_resources.md)

plans/T2T_implementation_plan.md:75

• These links are also relative to plans/ and will be broken as written; additionally, the LaTeX arrows in the validation bullet won’t render on GitHub.

### C. [`docs/oblx/docs/resources/human_resources.tsv`](docs/oblx/docs/resources/human_resources.tsv)
- **Resource Table**: Add new entries for the T2T reference genome, annotations, and liftovered VCFs to ensure traceability.

## 7. Integration & Testing
- **Path Mapping**: Update `get_pull_resources_output` in [`workflow/Snakefile`](workflow/Snakefile) to conditionally map T2T paths vs standard GRChx paths.

plans/T2T_implementation_plan.md:39

• More instances of \$\\rightarrow\$ appear in this section; since GitHub Markdown doesn’t render LaTeX math by default, replace these with a plain/unicode arrow to avoid the raw LaTeX showing up in rendered docs.

| **New** | `download_t2t_problematic_regions` | Download GIAB BigBed $\rightarrow$ convert to BED via `bigBedToBed`. | Use `use rule download_ucsc_data as ... with:`. <br> URL: `https://hgdownload.soe.ucsc.edu/gbdb/hs1/problematic/GIAB/alldifficultregions.bb` |
| **Redefined** | `download_repeat_masker` | Branch logic to support T2T sources instead of HG38-only paths. | Base rule $\rightarrow$ inherited T2T rule. |

## 3. Liftover Pipeline (GRCh38 $\rightarrow$ T2T)
Since native T2T resources for some tools are unavailable, a new sequence of rules is required:

[franla23]

Thanks, lgtm! Just wondering if it is better to maintain to have two independent workflow/rules/pull_resources.smk for hg38 and t2t as most of the rules have to be re-written.

[jonasfreimuth]

Current state of the discussion:

• Full support of the same set of features as is currently implemented for GRCh38 is a) large effort to implement as no 1:1 mapping of resources is available, leading to high workload in implementation b) not possible to the same coverage in terms of variant resources
• Partial support of mainly aligner indices would be relatively straightforward as that would only entail download of the annotated reference (but might still not be fully reporducible due to the unclear versioning strategy of the T2T assembly and annotation).