Skip to content
@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

Pinned Loading

  1. tools tools Public

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

    Python 327 267

  2. modules modules Public

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

    Nextflow 433 1.1k

  3. rnaseq rnaseq Public

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    Nextflow 1.4k 910

  4. sarek sarek Public

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

    Nextflow 614 564

  5. configs configs Public

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

    Nextflow 114 377

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 203 repositories
  • 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 614 MIT 564 259 (5 issues need help) 49 Updated Oct 24, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream's past year of commit activity
    Nextflow 118 MIT 69 12 2 Updated Oct 24, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 99 MIT 301 124 38 Updated Oct 24, 2026
  • stats Public

    nf-core in numbers

    nf-core/stats's past year of commit activity
    Python 2 4 45 15 Updated Oct 24, 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 18 8 1 Updated Oct 24, 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 23 MIT 6 19 1 Updated Oct 24, 2026
  • magmap Public

    Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

    nf-core/magmap's past year of commit activity
    Nextflow 13 MIT 6 16 0 Updated Oct 24, 2026
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler's past year of commit activity
    Nextflow 193 MIT 68 49 (1 issue needs help) 7 Updated Oct 24, 2026
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 327 MIT 266 371 95 Updated Oct 24, 2026
  • strict-syntax-health Public

    Track Nextflow strict syntax linting health across nf-core pipelines

    nf-core/strict-syntax-health's past year of commit activity
    Python 7 MIT 4 0 0 Updated Oct 24, 2026
View all repositories