[Verse 1] Snakemake rules chained like dominoes falling in line, Nextflow channels pumping data down the pipe just fine, nf-core hands you pipelines built by a hundred hands, WDL scripts run on Cromwell, portable where it lands, Containers pack the runtime so it never drifts or breaks, Docker or Singularity — pick the box the project takes, No more "worked on my laptop" — that excuse is dead, Reproducible means a stranger gets your same output instead. [Chorus] F-A-I-R, that's the flag we fly, Findable, Accessible, Interoperable, don't ask why, Reusable data, tested code, a pipeline built to run, Snakemake, Nextflow, Cromwell — three roads, same sun, Test it small before you scale it tall, Capstone calling, gonna answer the call. [Verse 2] Write a unit test before you trust a single line, Toy FASTQ with ten reads, checks the answer every time, Continuous integration, GitHub Actions on the clock, Every push gets vetted, every merge request gets rocked, Small test data, minutes not hours, running end to end, Green checkmark or you're debugging till the weekend, Assertions catch the silent bug before it hits the wild, Trust but verify — that's the rule for every child. [Verse 3] Streaming beats loading when the genome's ninety gig, Don't read the whole BAM file, that's an amateur's gig, htslib bindings, pysam whispers to the C, Vectorize with NumPy, let the loops run free, Profile your memory, find the leak before it drowns you, Parallelize across the cores, let the cluster crown you, Rust and C step in when Python starts to crawl, Compiled speed for inner loops, that's the protocol. [Verse 4] SRA, ENA, GEO — the data's public, free, dbGaP and EGA guard the human pedigree, Controlled access, consent forms, re-identification fear, A genotype can name a face if you're not careful here, MINSEQE keeps the metadata telling the story straight, Privacy before publication — that's a scientist's trait. [Bridge] IGV pulls up the pileup, JBrowse renders the track, UCSC browser shows the variant calling back, Figures clean, reports honest — methods, limits, QC too, Pick your capstone: germline VCF or a genome brand new, Bacteria assembled, AMR genes in the frame, Selection scans on populations, ATAC calling the flame, Tumor-normal variants, signatures inked in the scar, Six deliverables, one repo — that's how you go far. [Chorus] F-A-I-R, that's the flag we fly, Findable, Accessible, Interoperable, don't ask why, Reusable data, tested code, a pipeline built to run, Snakemake, Nextflow, Cromwell — three roads, same sun, Test it small before you scale it tall, Capstone calling, gonna answer the call. [Outro] README open, environment locked, the license clear, Push the final commit, thirty weeks landed here, From double helix theory to a report that ships, That's the DNA curriculum, mic drop, fingertips.
← Module 13 — Metagenomics, Pangenomics & Special Topics (Weeks 25–26) | Appendix A — Mathematical & Statistical Foundations (reference track) →