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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 329 269

  2. modules modules Public

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

    Nextflow 435 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 616 565

  5. configs configs Public

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

    Nextflow 114 378

  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
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 100 MIT 300 124 26 Updated Nov 3, 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 Nov 3, 2026
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar's past year of commit activity
    Nextflow 61 MIT 50 22 4 Updated Nov 2, 2026
  • cellpainting Public
    nf-core/cellpainting's past year of commit activity
    Nextflow 10 MIT 13 9 5 Updated Nov 2, 2026
  • 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 616 MIT 565 240 (5 issues need help) 50 Updated Nov 2, 2026
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    nf-core/airrflow's past year of commit activity
    Nextflow 83 MIT 58 47 11 Updated Nov 2, 2026
  • modules Public

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

    nf-core/modules's past year of commit activity
    Nextflow 435 MIT 1,131 296 (1 issue needs help) 202 Updated Nov 2, 2026
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair

    nf-core/methylseq's past year of commit activity
    Nextflow 201 MIT 185 29 12 Updated Nov 2, 2026
  • clipseq Public

    CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

    nf-core/clipseq's past year of commit activity
    Nextflow 26 MIT 43 48 9 Updated Nov 2, 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 Nov 2, 2026
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