Design and implementation of reproducible bioinformatics and ML pipelines using workflow managers (Snakemake, Nextflow), containers (Singularity/Apptainer, Docker), conda environments with lock files, data versioning (DVC), experiment tracking (MLflow, Weights & Biases), and FAIR-by-design principles. Covers when to choose each tool, HPC integration, and nf-core as a model of best practices. Use when designing a new pipeline, refactoring existing ad-hoc scripts into a reproducible workflow, or documenting an analysis for publication.
