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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 329 268

  2. modules modules Public

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

    Nextflow 434 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 910

  4. sarek sarek Public

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

    Nextflow 616 565

  5. configs configs Public

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

    Nextflow 114 378

  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
  • 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 616 MIT 565 246 (5 issues need help) 50 Updated Oct 30, 2026
  • 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 16 6 3 Updated Oct 30, 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 83 MIT 58 47 10 Updated Oct 30, 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 1,402 MIT 910 18 5 Updated Oct 30, 2026
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa's past year of commit activity
    Nextflow 22 MIT 7 4 2 Updated Oct 30, 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 434 MIT 1,131 290 (1 issue needs help) 199 Updated Oct 30, 2026
  • seqsubmit Public

    nf-core pipeline for data submission to ENA

    nf-core/seqsubmit's past year of commit activity
    Nextflow 22 MIT 11 20 4 Updated Oct 30, 2026
  • provenancereport Public

    Generate reproducible Quarto reports together with an audit trail of inputs, checksums, software versions, runtime environments, and provenance metadata.

    nf-core/provenancereport's past year of commit activity
    Nextflow 1 MIT 3 2 4 Updated Oct 30, 2026
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion's past year of commit activity
    Nextflow 176 MIT 128 25 (1 issue needs help) 6 Updated Oct 30, 2026
  • funcscan Public

    (Meta-)genome screening for functional and natural product gene sequences

    nf-core/funcscan's past year of commit activity
    Nextflow 119 MIT 39 17 1 Updated Oct 30, 2026
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