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nf-core · GitHub
nf-core
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Verified
We've verified that the organization nf-core controls the domain:
@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:
Pinned
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Python package with helper tools for the nf-core community.
Python
263
207
Repository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow
364
883
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Nextflow
1.1k
783
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Nextflow
462
459
Config files used to define parameters specific to compute environments at different Institutions
Nextflow
102
316
Where new ideas for nf-core pipelines, special interest groups and more are proposed
8
3
Repositories
Showing 10 of 169 repositories
website
Public
Code and files for the main nf-core website.
nf-core/website’s past year of commit activity
methylseq
Public
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
nf-core/methylseq’s past year of commit activity
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core/modules’s past year of commit activity
rnafusion
Public
RNA-seq analysis pipeline for detection of gene-fusions
nf-core/rnafusion’s past year of commit activity
tfactivity
Public
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
nf-core/tfactivity’s past year of commit activity
Nextflow
12
MIT
5
1
4
Updated Jul 26, 2025
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
nf-core/setup-nextflow’s past year of commit activity
TypeScript
19
MIT
6
5
7
Updated Jul 25, 2025
nf-core/cellpainting’s past year of commit activity
Nextflow
6
MIT
6
14
4
Updated Jul 25, 2025
rnadnavar
Public
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
nf-core/rnadnavar’s past year of commit activity
Nextflow
8
MIT
9
6
6
Updated Jul 25, 2025
ops
Public
Different *Ops related scripts for the nf-core org.
nf-core/ops’s past year of commit activity
Python
3
2
34
7
Updated Jul 25, 2025
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