Add REGENIE chunked step 1 modules#11739
Draft
lyh970817 wants to merge 17 commits into
Draft
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
REGENIE is a C++ program for whole-genome regression modelling of large GWAS cohorts. This PR adds a chunked Step 1 module family that exposes REGENIE's native level-0 parallelization workflow:
regenie/splitl0creates the level-0 split master file and per-job SNP lists.regenie/runl0runs one level-0 job from the split master file.regenie/runl1gathers the level-0 outputs and finishes Step 1, producing the standard prediction list and LOCO files consumed byregenie/step2.This PR depends on the base
regenie/step1module in #11008.PR checklist
topic: versions- See version_topicslabelnf-core modules test regenie/splitl0 --profile dockernf-core modules test regenie/runl0 --profile dockernf-core modules test regenie/runl1 --profile dockernf-core modules test regenie/splitl0 --profile singularitynf-core modules test regenie/runl0 --profile singularitynf-core modules test regenie/runl1 --profile singularitynf-core modules test regenie/splitl0 --profile condanf-core modules test regenie/runl0 --profile condanf-core modules test regenie/runl1 --profile conda