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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 ).
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Python package with helper tools for the nf-core community.
Python
285
224
Repository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow
393
953
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Nextflow
1.2k
834
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Nextflow
533
500
Config files used to define parameters specific to compute environments at different Institutions
Nextflow
107
339
Where new ideas for nf-core pipelines, special interest groups and more are proposed
8
3
Repositories
Showing 10 of 179 repositories
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
nf-core/scdownstream’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
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core/modules’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
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
nf-core/configs’s past year of commit activity
nf-core/strict-syntax-health’s past year of commit activity
Python
4
MIT
1
0
0
Updated Jan 17, 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
rnavar
Public
gatk4 RNA variant calling pipeline
nf-core/rnavar’s past year of commit activity
Nextflow
58
MIT
43
19
2
Updated Jan 16, 2026
tools
Public
Python package with helper tools for the nf-core community.
nf-core/tools’s past year of commit activity
nf-core/setup-nextflow’s past year of commit activity
TypeScript
24
MIT
4
5
11
Updated Jan 16, 2026
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