snRNA-seq Sex Validation & Stratified Integration Pipeline

This Nextflow pipeline processes single-nucleus RNA-seq data from ASAP Collaborative Research Network cohorts for downstream Y-chromosome expression analysis. Its key contribution is **automated sex metadata curation**: each donor is independently validated using XIST expression and a chrY gene score, flagging and excluding mislabeled samples before integration which is a critical quality step for any sex-stratified or Y-chromosome-focused analysis. The pipeline also performs ambient RNA correction (SoupX), per-sample quality control (scrublet, adaptive filters), and sex-stratified dataset integration via Harmony (CPU) or scVI (GPU). Developed as part of the **ASAP Multi-Omics Meta-Analysis (MoMa)** project *Chromosome Y Associated Transcriptional Variation in Parkinson’s Disease*.