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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 331 268

  2. modules modules Public

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

    Nextflow 437 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 911

  4. sarek sarek Public

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

    Nextflow 621 565

  5. configs configs Public

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

    Nextflow 114 380

  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
  • modules Public

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

    nf-core/modules's past year of commit activity
    Nextflow 437 MIT 1,143 293 (1 issue needs help) 144 Updated Nov 12, 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 621 MIT 565 238 (5 issues need help) 42 Updated Nov 12, 2026
  • seqinspector Public

    Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.

    nf-core/seqinspector's past year of commit activity
    Nextflow 28 MIT 46 27 3 Updated Nov 12, 2026
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex's past year of commit activity
    Nextflow 61 MIT 57 18 (1 issue needs help) 2 Updated Nov 12, 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 8 (1 issue needs help) 1 Updated Nov 12, 2026
  • agents Public
    nf-core/agents's past year of commit activity
    0 MIT 4 2 9 Updated Nov 12, 2026
  • abotyper Public

    A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.

    nf-core/abotyper's past year of commit activity
    Nextflow 5 MIT 2 1 1 Updated Nov 12, 2026
  • bamtofastq Public

    Converts bam or cram files to fastq format and does quality control.

    nf-core/bamtofastq's past year of commit activity
    Nextflow 32 MIT 17 9 3 Updated Nov 12, 2026
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval's past year of commit activity
    Nextflow 31 MIT 11 4 0 Updated Nov 12, 2026
  • nanostring Public

    An analysis pipeline for Nanostring nCounter expression data.

    nf-core/nanostring's past year of commit activity
    Nextflow 18 MIT 15 3 2 Updated Nov 12, 2026
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