| name | nextflow |
| description | Nextflow — workflow manager for scalable, reproducible bioinformatics pipelines (DSL2, containers, cloud/HPC executors). Use when packaging shotgun metagenomics stages into portable runs or adopting nf-core modules/pipelines. Upstream: https://github.com/nextflow-io/nextflow · https://nf-co.re. Route via research-analysis / metagenomics-workflow / setup. Alternative: snakemake.
|
| license | MIT |
| category | utilities |
| tags | ["Nextflow","nf-core","workflow","reproducibility","pipeline","HPC"] |
| upstream | https://github.com/nextflow-io/nextflow |
| stage | utilities |
Nextflow
Upstream: nextflow-io/nextflow ·
nf-core: https://nf-co.re · Docs: https://www.nextflow.io/docs/latest/
Citation
Di Tommaso, P. et al. Nextflow enables reproducible computational workflows.
Nat. Biotechnol. 35, 316–319 (2017).
https://doi.org/10.1038/nbt.3820
nf-core: Ewels, P. A. et al. The nf-core framework for community-curated
bioinformatics pipelines. Nat. Biotechnol. 38, 276–278 (2020).
https://doi.org/10.1038/s41587-020-0439-x
See also docs/references.md.
Analytical thinking
Nextflow orchestrates containerized processes with resumable execution —
ideal once tool choices from tool-selection are fixed. Prefer nf-core
pipelines/modules when they match your claim; otherwise write a thin DSL2
wrapper around this package’s skills. Pin Nextflow version, container engine
(Docker/Singularity/Apptainer), and nextflow.config profiles for HPC.
Workflow ≠ statistical Methods — still pin each bioinformatics tool/DB inside
processes.
How to run
nextflow run nf-core/<pipeline> -profile singularity --input samplesheet.csv ...
Decision tree
Need reproducible pipeline orchestration?
├─ Nextflow / nf-core → nextflow
├─ Python/Snakefile ecosystem → snakemake
└─ Ad-hoc scripts only → setup + stage skills
Related skills
snakemake · setup · metagenomics-workflow · research-analysis ·
tool-selection · multiqc
