Conversation
There was a problem hiding this comment.
Pull request overview
Adds a minimal HDL-formatted shared fixture set (HDL LD reference layout + canonical sumstats) to support companion module tests that require HDL reference directory structure.
Changes:
- Added toy canonical HDL summary statistics for two traits.
- Added toy HDL LD reference
.bimsidecars for two chr1 chunks. - Documented the new HDL fixture files in the root
README.md.
Reviewed changes
Copilot reviewed 5 out of 9 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| data/genomics/homo_sapiens/popgen/hdl/sumstats/trait1_canonical.tsv | Adds toy canonical HDL summary statistics (trait 1) |
| data/genomics/homo_sapiens/popgen/hdl/sumstats/trait2_canonical.tsv | Adds toy canonical HDL summary statistics (trait 2) |
| data/genomics/homo_sapiens/popgen/hdl/reference/chr1.1_toy.bim | Adds toy HDL reference BIM sidecar for chunk 1.1 |
| data/genomics/homo_sapiens/popgen/hdl/reference/chr1.2_toy.bim | Adds toy HDL reference BIM sidecar for chunk 1.2 |
| README.md | Documents the newly added HDL fixture files |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
You can also share your feedback on Copilot code review. Take the survey.
| rs2 C T 1 202 rs2 C T 10000 -0.2 | ||
| rs3 A C 1 303 rs3 A C 10000 0.4 | ||
| rs4 G T 1 404 rs4 G T 10000 -0.1 |
| rs1 A G 1 101 rs1 A G 12000 0.3 | ||
| rs2 C T 1 202 rs2 C T 12000 -0.4 | ||
| rs3 A C 1 303 rs3 A C 12000 0.2 | ||
| rs4 G T 1 404 rs4 G T 12000 -0.2 |
There was a problem hiding this comment.
Pull request overview
Adds a minimal synthetic HDL-format reference + sumstats fixture set to support companion HDL module tests, along with regeneration tooling and documentation.
Changes:
- Added toy HDL reference sidecars/payloads and canonical sumstats TSVs under
data/genomics/homo_sapiens/popgen/hdl/. - Added an R script to regenerate the fixtures deterministically from in-repo constants.
- Documented the dataset locally and registered the new files in the root
README.md.
Reviewed changes
Copilot reviewed 7 out of 11 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| data/genomics/homo_sapiens/popgen/hdl/sumstats/trait2_canonical.tsv | Adds toy canonical sumstats fixture for trait 2 |
| data/genomics/homo_sapiens/popgen/hdl/sumstats/trait1_canonical.tsv | Adds toy canonical sumstats fixture for trait 1 |
| data/genomics/homo_sapiens/popgen/hdl/reference/chr1.2_toy.bim | Adds toy BIM sidecar for HDL chunk 1.2 |
| data/genomics/homo_sapiens/popgen/hdl/reference/chr1.1_toy.bim | Adds toy BIM sidecar for HDL chunk 1.1 |
| data/genomics/homo_sapiens/popgen/hdl/generate_toy_hdl_data.R | Adds generator script for recreating all toy fixtures |
| data/genomics/homo_sapiens/popgen/hdl/README.md | Documents intent, layout, and regeneration steps for the HDL toy dataset |
| README.md | Registers the new HDL toy dataset files in the root inventory |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
You can also share your feedback on Copilot code review. Take the survey.
README.md
Outdated
| - hdl/reference/chr1.1_toy.bim: Toy HDL LD reference BIM sidecar for chunk 1.1. From [HDL](https://github.com/zhenin/HDL). | ||
| - hdl/reference/chr1.1_toy.rda: Toy HDL LD reference payload for chunk 1.1. From [HDL](https://github.com/zhenin/HDL). | ||
| - hdl/reference/chr1.2_toy.bim: Toy HDL LD reference BIM sidecar for chunk 1.2. From [HDL](https://github.com/zhenin/HDL). | ||
| - hdl/reference/chr1.2_toy.rda: Toy HDL LD reference payload for chunk 1.2. From [HDL](https://github.com/zhenin/HDL). | ||
| - hdl/reference/toy_snp_counter.RData: Toy HDL SNP count metadata. From [HDL](https://github.com/zhenin/HDL). | ||
| - hdl/reference/toy_snp_list.RData: Toy HDL SNP list metadata. From [HDL](https://github.com/zhenin/HDL). | ||
| - hdl/sumstats/trait1_canonical.tsv: Canonical HDL summary statistics for trait 1. From [HDL](https://github.com/zhenin/HDL). | ||
| - hdl/sumstats/trait2_canonical.tsv: Canonical HDL summary statistics for trait 2. From [HDL](https://github.com/zhenin/HDL). |
There was a problem hiding this comment.
Updated the root README entries to describe these as synthetic HDL-format fixtures generated by generate_toy_hdl_data.R for HDL-compatible inputs, and aligned the PR body wording/checklist with that provenance.
|
|
||
| args <- commandArgs(trailingOnly = FALSE) | ||
| file_arg <- "--file=" | ||
| script_path <- sub(file_arg, "", args[grep(file_arg, args)]) |
| "1 rs1 0 101 A G", | ||
| "1 rs2 0 102 C T" | ||
| ), | ||
| file.path(reference_dir, "chr1.1_toy.bim") | ||
| ) | ||
|
|
||
| writeLines( | ||
| c( | ||
| "1 rs3 0 201 A C", | ||
| "1 rs4 0 202 G T" |
PR checklist
README.mdREADME.mdis still up-to-dateThis PR adds the smallest shared HDL fixture set needed to exercise HDL-compatible LD reference inputs for the companion module submission.
Existing
popgenfixtures do not provide the HDL reference directory layout consumed byhdl/h2andhdl/rg.All HDL files in this branch are fully synthetic toy fixtures generated in-repo by
data/genomics/homo_sapiens/popgen/hdl/generate_toy_hdl_data.Rto match HDL's expected format and layout; they are compatible with HDL inputs and do not redistribute an upstream HDL reference bundle.Added files:
reference/chr1.1_toy.bimreference/chr1.1_toy.rdareference/chr1.2_toy.bimreference/chr1.2_toy.rdareference/toy_snp_counter.RDatareference/toy_snp_list.RDatasumstats/trait1_canonical.tsvsumstats/trait2_canonical.tsvSize footprint: 915 bytes total.
These toy HDL inputs were minimized to the smallest set that still supports real HDL execution for the companion module tests.
Companion modules PR: nf-core/modules#10912