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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 327 265

  2. modules modules Public

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

    Nextflow 432 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 905

  4. sarek sarek Public

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

    Nextflow 614 562

  5. configs configs Public

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

    Nextflow 114 376

  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
  • nf-core-utils Public

    Nextflow plugin with nf-core utility functions

    nf-core/nf-core-utils's past year of commit activity
    Groovy 1 Apache-2.0 1 21 7 Updated Oct 17, 2026
  • msproteomics Public
    nf-core/msproteomics's past year of commit activity
    Nextflow 0 MIT 1 0 3 Updated Oct 17, 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 1,390 MIT 905 22 7 Updated Oct 17, 2026
  • circrna Public

    circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

    nf-core/circrna's past year of commit activity
    Nextflow 61 MIT 33 29 2 Updated Oct 17, 2026
  • spatialaxe Public

    A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

    nf-core/spatialaxe's past year of commit activity
    Python 46 MIT 26 49 13 Updated Oct 17, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 99 MIT 301 125 29 Updated Oct 17, 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 432 MIT 1,123 292 (1 issue needs help) 192 Updated Oct 17, 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 17, 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 82 MIT 58 45 11 Updated Oct 16, 2026
  • pathogenepidemiology Public

    [DEVELOPMENT UNDERWAY] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

    nf-core/pathogenepidemiology's past year of commit activity
    Nextflow 3 MIT 2 12 (2 issues need help) 0 Updated Oct 16, 2026
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