Claude/snakemake phenotype pipeline 1 dnkm#1294
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hsun3163 merged 2 commits intoStatFunGen:mainfrom Mar 1, 2026
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…/sos to route3 notebooks New scripts in renovated_code/: - pecotmr_integration/univariate_plot.R — SuSiE PIP/z-score plots - data_preprocessing/genotype/GWAS_QC.R — kinship-based sample removal (king_2) - molecular_phenotypes/calling/RNA_calling.py — merge per-sample RNA-SeQC GCT outputs - molecular_phenotypes/calling/RNA_calling.R — aggregate Picard alignment/RNA/dup metrics route3/transform_notebooks.py: - Add transforms for GWAS_QC king_2 (rscript), RNA_calling rnaseqc_call_2 (python3), RNA_calling rsem_call_4/rnaseqc_call_4 (rscript), rss_analysis univariate_plot (rscript) - Regenerate all 14 route3/notebooks/ — no more inline R/Python for pipeline-critical steps Snakefile + rules/sos/: - Add ROUTE3_NOTEBOOKS and RENOVATED_CODE variables to Snakefile - Update all 6 rules/sos/*.smk to call route3/notebooks/ instead of pipeline/ and add --renovated-code-dir to every sos run invocation https://claude.ai/code/session_017a1quThNAyMvWRAdDonQkB
Relocates code/snakemake_pipeline/ → renovated_code/snakemake/ so that all pipeline code (Snakemake rules, route3 notebooks, transform script, config, profiles, dryrun fixtures) lives alongside the modular R/Python scripts it orchestrates. No path-logic changes required: the Snakefile computes RENOVATED_CODE as _SNAKEFILE_DIR.parent.parent / "renovated_code", which resolves to the same repo-root-relative path from the new location. https://claude.ai/code/session_017a1quThNAyMvWRAdDonQkB
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