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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 322 255

  2. modules modules Public

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

    Nextflow 429 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 604 550

  5. configs configs Public

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

    Nextflow 112 375

  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
  • 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 23, 2026
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq's past year of commit activity
    Nextflow 101 MIT 138 23 (2 issues need help) 3 Updated Sep 22, 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 1,371 MIT 897 13 3 Updated Sep 22, 2026
  • chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    nf-core/chipseq's past year of commit activity
    Nextflow 245 MIT 184 17 3 Updated Sep 22, 2026
  • hlatyping Public

    Precision HLA typing from next-generation sequencing data

    nf-core/hlatyping's past year of commit activity
    Nextflow 81 MIT 40 9 2 Updated Sep 22, 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 604 MIT 550 258 (5 issues need help) 40 Updated Sep 22, 2026
  • 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 56 MIT 21 7 1 Updated Sep 22, 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 15 1 Updated Sep 22, 2026
  • provenancereport Public

    A simple provenance reporting pipeline

    nf-core/provenancereport's past year of commit activity
    Nextflow 1 MIT 3 1 1 Updated Sep 22, 2026
  • rnasplice Public

    rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

    nf-core/rnasplice's past year of commit activity
    Nextflow 69 MIT 40 7 1 Updated Sep 22, 2026
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