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 322 255

  2. modules modules Public

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

    Nextflow 430 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 897

  4. sarek sarek Public

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

    Nextflow 605 553

  5. configs configs Public

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

    Nextflow 112 374

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 201 repositories
  • proteinannotator Public

    Generation of sequence-level annotations for amino acid sequences

    nf-core/proteinannotator's past year of commit activity
    Nextflow 15 MIT 12 22 4 Updated Sep 27, 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 115 MIT 66 24 (2 issues need help) 1 Updated Sep 27, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 98 MIT 298 122 20 Updated Sep 27, 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 Sep 27, 2026
  • msproteomics Public
    nf-core/msproteomics's past year of commit activity
    Nextflow 0 MIT 0 0 1 Updated Sep 27, 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 24 MIT 10 9 5 Updated Sep 26, 2026
  • taxmarker Public

    Identify taxonomically mislabelled sequences

    nf-core/taxmarker's past year of commit activity
    Nextflow 1 MIT 1 11 1 Updated Sep 26, 2026
  • metatdenovo Public

    Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

    nf-core/metatdenovo's past year of commit activity
    Nextflow 36 MIT 21 23 2 Updated Sep 26, 2026
  • rnaseq Public

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

    nf-core/rnaseq's past year of commit activity
    Nextflow 1,374 MIT 897 22 5 Updated Sep 26, 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 430 MIT 1,102 305 (1 issue needs help) 172 Updated Sep 26, 2026
View all repositories