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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 275 215

  2. modules modules Public

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

    Nextflow 379 912

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 804

  4. sarek sarek Public

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

    Nextflow 492 485

  5. configs configs Public

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

    Nextflow 104 332

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 172 repositories
  • createpanelrefs Public

    Generate Panel of Normals, models or other similar references from lots of samples

    nf-core/createpanelrefs’s past year of commit activity
    Nextflow 11 MIT 10 6 3 Updated Oct 24, 2025
  • ops Public

    Different *Ops related scripts for the nf-core org.

    nf-core/ops’s past year of commit activity
    Python 3 2 37 16 Updated Oct 24, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 275 MIT 215 315 33 Updated Oct 24, 2025
  • isoseq Public

    Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

    nf-core/isoseq’s past year of commit activity
    Nextflow 48 MIT 21 9 1 Updated Oct 24, 2025
  • rarevariantburden Public

    Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.

    nf-core/rarevariantburden’s past year of commit activity
    Nextflow 0 MIT 2 0 2 Updated Oct 24, 2025
  • pixelator Public

    Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

    nf-core/pixelator’s past year of commit activity
    Nextflow 12 MIT 8 2 2 Updated Oct 24, 2025
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 84 MIT 53 90 (1 issue needs help) 10 Updated Oct 24, 2025
  • nf-core-utils Public

    Nextflow plugin for nf-core utils

    nf-core/nf-core-utils’s past year of commit activity
    Groovy 1 Apache-2.0 0 10 6 Updated Oct 24, 2025
  • 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 492 MIT 485 302 (6 issues need help) 36 Updated Oct 24, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 253 102 25 Updated Oct 24, 2025
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