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@nf-core

nf-core

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

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  1. tools tools Public

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

    Python 328 268

  2. modules modules Public

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

    Nextflow 434 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 615 566

  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
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 328 MIT 268 369 101 Updated Oct 29, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 100 MIT 301 125 32 Updated Oct 29, 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 29, 2026
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease's past year of commit activity
    Nextflow 126 MIT 71 12 8 Updated Oct 28, 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 28, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag's past year of commit activity
    Nextflow 325 MIT 161 79 (1 issue needs help) 7 Updated Oct 28, 2026
  • epitopeprediction Public

    A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

    nf-core/epitopeprediction's past year of commit activity
    Nextflow 56 MIT 35 6 (1 issue needs help) 2 Updated Oct 28, 2026
  • abotyper Public

    A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.

    nf-core/abotyper's past year of commit activity
    Python 4 MIT 2 0 10 Updated Oct 28, 2026
  • detaxizer Public

    A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

    nf-core/detaxizer's past year of commit activity
    Nextflow 26 MIT 10 7 1 Updated Oct 28, 2026
  • epigenomesegmentation Public

    An nf-core pipeline for epigenome segmentation using EpiSegMix/Meth — a hidden Markov model with flexible read count distributions and state duration modeling for histone, open chromatin, and methylation signals.

    nf-core/epigenomesegmentation's past year of commit activity
    Makefile 1 MIT 1 0 3 Updated Oct 28, 2026
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