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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 438 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
  • 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 4 22 12 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 565 235 (5 issues need help) 48 Updated Nov 12, 2026
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq's past year of commit activity
    Nextflow 104 MIT 140 33 (2 issues need help) 1 Updated Nov 12, 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 438 MIT 1,144 294 (1 issue needs help) 149 Updated Nov 12, 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 1,407 MIT 911 17 6 Updated Nov 12, 2026
  • deepmutscan Public

    nf-core/deepmutscan is a reproducible, scalable, and community-curated pipeline for analyzing deep mutational scanning (DMS) data using shotgun DNA sequencing.

    nf-core/deepmutscan's past year of commit activity
    Nextflow 5 MIT 5 16 3 Updated Nov 12, 2026
  • seqsubmit Public

    nf-core pipeline for data submission to ENA

    nf-core/seqsubmit's past year of commit activity
    Nextflow 22 MIT 11 14 3 Updated Nov 12, 2026
  • spatialvi Public

    Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

    nf-core/spatialvi's past year of commit activity
    Nextflow 82 MIT 41 3 5 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 4 Updated Nov 12, 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 201 MIT 185 27 8 Updated Nov 12, 2026
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