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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 324 258

  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 901

  4. sarek sarek Public

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

    Nextflow 609 557

  5. configs configs Public

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

    Nextflow 113 375

  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
  • 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 70 16 7 Updated Oct 3, 2026
  • cageseq Public

    CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

    nf-core/cageseq's past year of commit activity
    Nextflow 11 MIT 12 10 5 Updated Oct 3, 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 199 MIT 181 26 8 Updated Oct 3, 2026
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler's past year of commit activity
    Nextflow 192 MIT 69 51 (1 issue needs help) 5 Updated Oct 3, 2026
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies's past year of commit activity
    Nextflow 23 MIT 4 10 1 Updated Oct 3, 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 1,109 303 (1 issue needs help) 172 Updated Oct 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 Oct 3, 2026
  • plasmodiumdrugres Public

    Pipeline for analyzing drug resistance markers from Plasmodium microhaplotype data. It translates variants into amino acid changes at drug resistance loci and estimates allele frequencies and prevalences at both single-locus and multi-locus levels. Microhaplotype data can be supplied in the form of an allele table or a PMO file.

    nf-core/plasmodiumdrugres's past year of commit activity
    Nextflow 2 MIT 2 9 6 Updated Oct 3, 2026
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    nf-core/test-datasets's past year of commit activity
    163 MIT 536 43 34 Updated Oct 2, 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 1,378 MIT 901 25 8 Updated Oct 2, 2026
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