What is Nextflow? Concepts and Use Cases Available Beginner
Understand why workflow managers exist, how Nextflow solves reproducibility and scalability challenges, and where it fits in the modern bioinformatics ecosystem.
Installing Nextflow and Java Available Beginner
Install Java (required runtime), download the Nextflow launcher, verify your setup, and configure the environment on Linux, macOS, and WSL2.
Hello World: Your First Nextflow Pipeline Available Beginner
Write and run a minimal pipeline, understand the working directory layout, interpret Nextflow output logs, and resume a run with -resume.
Processes and Channels Coming Soon Beginner
Learn the two core abstractions: processes (execution units) and channels (data streams). Define inputs, outputs, and scripts inside a process block.
Operators and Data Transformations Coming Soon Intermediate
Transform channel contents with operators such as map, filter, collect, groupTuple, and combine to build complex data flows.
Configuration Files and Execution Profiles Coming Soon Intermediate
Use nextflow.config to set resource requirements, container images, and executor settings. Switch between local, SLURM, and cloud profiles.
Running Pipelines with Docker Coming Soon Intermediate
Enable Docker in Nextflow, pull and specify container images per process, and understand how Nextflow mounts work directories inside containers.
Using Singularity on HPC Clusters Coming Soon Intermediate
Convert Docker images to Singularity SIF files, configure Singularity cache and bind paths, and run containerised pipelines on shared HPC systems.
Conda Environments in Nextflow Coming Soon Beginner
Define per-process conda environments using YAML files or channel directives, and compare the trade-offs between conda, Docker, and Singularity.
Introduction to nf-core Coming Soon Beginner
Explore the nf-core community, browse available pipelines on nf-core.re, understand the release cycle and versioning, and learn nf-core conventions.
Running nf-core/rnaseq Coming Soon Intermediate
Download and run the nf-core/rnaseq pipeline end-to-end: prepare a samplesheet CSV, choose a reference genome, set resource profiles, and interpret MultiQC output.
nf-core Tools: Create, Lint, and Update Pipelines Coming Soon Intermediate
Install nf-core/tools, scaffold a new pipeline with nf-core create, run nf-core lint to check compliance, and sync with the latest nf-core template.
Modular Pipeline Design with DSL2 Modules Coming Soon Advanced
Structure reusable process modules, import them with include, and compose subworkflows to build maintainable, production-grade pipelines.
Testing Pipelines with nf-test Coming Soon Advanced
Write unit tests for processes and integration tests for workflows using nf-test. Run tests locally and in CI via GitHub Actions.
Submitting Pipelines to nf-core Coming Soon Advanced
Follow the nf-core contribution guide, pass all linting checks, open a pull request, and navigate the peer review process for community pipeline acceptance.