This skill should be used when the user asks to "build a genomics pipeline", "pick an nf-core pipeline", "which aligner/variant caller should I use", "analyze RNA-seq", "analyze single-cell RNA-seq", "annotate variants", "interpret variants with ACMG criteria", "detect CNVs", "call structural variants", or when choosing tools, file formats, and QC thresholds for NGS data. Provides opinionated tool defaults (aligners, variant callers, annotators), genomics file-format and reproducibility conventions, an nf-core pipeline selection table, and detailed references for RNA-seq (bulk and single-cell), variant annotation with clinical interpretation, and CNV/SV analysis. It does not teach Nextflow DSL2, Snakemake, or WDL authoring — for writing workflow code by hand, use those frameworks' own documentation.