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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

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tools tools Public

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

Python 331 268
modules modules Public

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

Nextflow 437 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 911
sarek sarek Public

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

Nextflow 621 565
configs configs Public

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

Nextflow 114 380
proposals proposals Public

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

10 6

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Showing 10 of 203 repositories

seqinspector Public
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.

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

Nextflow 28 MIT 46 27 3 Updated Nov 12, 2026
scrnaseq Public
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

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

Nextflow 365 MIT 235 59 (1 issue needs help) 7 Updated Nov 12, 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 437 MIT 1,143 293 (1 issue needs help) 144 Updated Nov 12, 2026
references Public
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

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

Nextflow 24 MIT 5 20 0 Updated Nov 12, 2026
nft-utils Public
nf-test utility functions

nf-core/nft-utils's past year of commit activity

Java 13 MIT 11 16 2 Updated Nov 12, 2026
rnavar Public
gatk4 RNA variant calling pipeline

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

Nextflow 62 MIT 50 22 4 Updated Nov 12, 2026
bamtofastq Public
Converts bam or cram files to fastq format and does quality control.

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

Nextflow 32 MIT 17 9 3 Updated Nov 12, 2026
fetchngs Public
Pipeline to fetch metadata and raw FastQ files from public databases

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

Nextflow 202 MIT 96 42 8 Updated Nov 12, 2026
setup-nextflow Public
A GitHub action to install Nextflow

nf-core/setup-nextflow's past year of commit activity

TypeScript 31 MIT 5 4 11 Updated Nov 12, 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 621 MIT 565 237 (5 issues need help) 42 Updated Nov 12, 2026

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nextflow nf-core pipeline workflow bioinformatics