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<#1932 Add HDL shared test fixtures> Pull request ...
# test-data
g
#1932 Add HDL shared test fixtures Pull request opened by lyh970817 PR checklist • I read the test-data specifications • I tried testing my module with available data and there is no compatible data in test-datasets • If I added data: I described the new files on the root 
README.md
• If I modified data: I checked whether the root 
README.md
is still up-to-date • I made sure to submit the smallest dataset possible (e.g. try .tar.gz for larger directories) This PR adds the smallest shared HDL fixture set needed to exercise HDL-compatible LD reference inputs for the companion module submission. Existing 
popgen
fixtures do not provide the HDL reference directory layout consumed by 
hdl/h2
and 
hdl/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.R
to 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.bim
• 
reference/chr1.1_toy.rda
• 
reference/chr1.2_toy.bim
• 
reference/chr1.2_toy.rda
• 
reference/toy_snp_counter.RData
• 
reference/toy_snp_list.RData
• 
sumstats/trait1_canonical.tsv
• 
sumstats/trait2_canonical.tsv
Size 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 nf-core/test-datasets
Review on #1932 Add HDL shared test fixtures Review comment by Copilot on lyh970817's pull request 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 
.bim
sidecars 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 | --- 💡 </nf-core/test-datasets/new/master?filename=.github/instructions/*.instructions.md|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. nf-core/test-datasets
Review on #1932 Add HDL shared test fixtures Review comment by Copilot on lyh970817's pull request 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 | --- 💡 </nf-core/test-datasets/new/master?filename=.github/instructions/*.instructions.md|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. nf-core/test-datasets
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