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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
264
208
Repository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow
367
885
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Nextflow
1.1k
786
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Nextflow
464
459
Config files used to define parameters specific to compute environments at different Institutions
Nextflow
103
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
pairgenomealign
Public
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
nf-core/pairgenomealign’s past year of commit activity
Nextflow
9
MIT
5
12
0
Updated Jul 31, 2025
ops
Public
Different *Ops related scripts for the nf-core org.
nf-core/ops’s past year of commit activity
Python
3
2
36
8
Updated Jul 31, 2025
nf-core/setup-nextflow’s past year of commit activity
TypeScript
20
MIT
6
5
7
Updated Jul 31, 2025
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core/modules’s past year of commit activity
sammyseq
Public
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
nf-core/sammyseq’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
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
variantbenchmarking
Public
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
nf-core/variantbenchmarking’s past year of commit activity
Nextflow
32
MIT
15
23
1
Updated Jul 30, 2025
viralmetagenome
Public
Detect iSNV and construct whole viral genomes from metagenomic samples
nf-core/viralmetagenome’s past year of commit activity
Nextflow
20
MIT
3
9
2
Updated Jul 30, 2025
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