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Bioinformatics Pipeline Automation — Snakemake, Nextflow & Galaxy Training | Reproducible Workflows

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> AI/ML, Data Science, Pipelines & Cloud >> Bioinformatics Pipeline Automation — Snakemake, Nextflow & Galaxy Training | Reproducible Workflows

Bioinformatics Pipeline Automation — Snakemake • Nextflow • Galaxy — Hands-on

Build production-grade, reproducible pipelines for genomics, transcriptomics, metagenomics and more using Snakemake, Nextflow and Galaxy. Learn workflow design patterns, containerized environments, HPC/Cloud execution, caching/checkpointing, provenance tracking, and CI/CD—with a mini capstone that ships a validated pipeline and report.

Bioinformatics Pipeline Automation — Snakemake • Nextflow • Galaxy
Help Desk · WhatsApp
Session 1
Fee: Rs 16,200
Workflow Design & Reproducibility
  • DAG thinking & modular patterns
    • rules/processes fan-in/out scatter–gather
  • Environments & containers
    • Conda/Mamba Docker/Singularity image pinning
  • Provenance & data contracts
    • checksums/manifests schema validation metadata capture
Session 2
Fee: Rs 21,800
Snakemake & Nextflow Essentials
  • Snakemake in practice
    • rules/wildcards profiles/clusters checkpoints/cache
  • Nextflow in practice
    • process/channel DSL2/modules nf-core usage
  • Error handling & testing
    • retries/resume unit tests/mocks fixtures/snapshots
Session 3
Fee: Rs 27,800
Galaxy, HPC/Cloud & Operations
  • Galaxy workflows & tool shed
    • histories/datasets workflow editor Galaxy flavors
  • Executors & scaling
    • SLURM/PBS Kubernetes cloud buckets/S3
  • Ops, monitoring & artifacts
    • MultiQC/reports logging/metrics artifact registries
Session 4
Fee: Rs 34,400
Mini Capstone: Publishable Pipeline
  • Ship a containerized NGS/omics pipeline (Snakemake or Nextflow)
    • Theory + Practical
  • CI/CD & reproducibility
    • GitHub Actions versioned releases param schemas
  • Deliverables: repo, images & runbook
    • code + tests Docker/Singularity PDF/HTML report


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