nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

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Overview
Repositories
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README.md

Welcome to @nf-core!

@nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow (@nextflow-io).

Here's how to get started:

📚 See available pipelines on the website.
👩‍💻 Check out the documentation.
🙋‍♀️ Come and say hi on our Slack!
🍿 Tune in for talks and events, get involved!
🌈 Please abide by our community code of conduct

Pinned Loading

tools tools Public

Python package with helper tools for the nf-core community.

Python 319 250
modules modules Public

Repository to host tool-specific module files for the Nextflow DSL2 community!

Nextflow 425 1.1k
rnaseq rnaseq Public

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Nextflow 1.4k 891
sarek sarek Public

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Nextflow 595 545
configs configs Public

Config files used to define parameters specific to compute environments at different Institutions

Nextflow 111 375
proposals proposals Public

Where new ideas for nf-core pipelines, special interest groups and more are proposed

10 6

Repositories

Type Language Sort

raredisease Public
Call and score variants from WGS/WES of rare disease patients.

nf-core/raredisease's past year of commit activity

Nextflow 122 MIT 70 25 10 Updated Aug 28, 2026
sarek Public
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

nf-core/sarek's past year of commit activity

Nextflow 595 MIT 545 255 (5 issues need help) 39 Updated Aug 28, 2026
website Public
Code and files for the main nf-core website.

nf-core/website's past year of commit activity

MDX 98 MIT 296 118 37 Updated Aug 28, 2026
metatdenovo Public
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

nf-core/metatdenovo's past year of commit activity

Nextflow 36 MIT 21 19 0 Updated Aug 28, 2026
phyloplace Public
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

nf-core/phyloplace's past year of commit activity

Nextflow 12 MIT 4 2 0 Updated Aug 28, 2026
modules Public
Repository to host tool-specific module files for the Nextflow DSL2 community!

nf-core/modules's past year of commit activity

Nextflow 425 MIT 1,096 317 (1 issue needs help) 172 Updated Aug 28, 2026
mspepid Public
This pipeline performs the peptide identification of MS2 spectra from a proteomics experiment. For this, different search algorithm and rescoring approaches can be selected.

nf-core/mspepid's past year of commit activity

Nextflow 3 MIT 1 3 1 Updated Aug 28, 2026
provenancereport Public
A simple provenance reporting pipeline

nf-core/provenancereport's past year of commit activity

Nextflow 1 MIT 3 6 1 Updated Aug 28, 2026
test-datasets Public
Test data to be used for automated testing with the nf-core pipelines

nf-core/test-datasets's past year of commit activity

164 MIT 527 44 35 Updated Aug 28, 2026
funcscan Public
(Meta-)genome screening for functional and natural product gene sequences

nf-core/funcscan's past year of commit activity

Nextflow 118 MIT 38 19 1 Updated Aug 28, 2026