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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:
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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
884
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Nextflow
1.1k
784
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Nextflow
463
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
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core/modules’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
website
Public
Code and files for the main nf-core website.
nf-core/website’s past year of commit activity
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
nf-core/oncoanalyser’s past year of commit activity
Nextflow
78
MIT
22
24
4
Updated Jul 29, 2025
tools
Public
Python package with helper tools for the nf-core community.
nf-core/tools’s past year of commit activity
epitopeprediction
Public
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
nf-core/epitopeprediction’s past year of commit activity
Nextflow
46
MIT
26
12
0
Updated Jul 28, 2025
pixelator
Public
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
nf-core/pixelator’s past year of commit activity
Nextflow
10
MIT
6
1
1
Updated Jul 28, 2025
nf-core/proteinfamilies’s past year of commit activity
Nextflow
14
MIT
3
4
0
Updated Jul 28, 2025
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
nf-core/scdownstream’s past year of commit activity
sopa
Public
Nextflow version of Sopa - spatial omics pipeline and analysis
nf-core/sopa’s past year of commit activity
Nextflow
4
MIT
1
0
1
Updated Jul 28, 2025
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