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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 323 255

  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 898

  4. sarek sarek Public

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

    Nextflow 607 555

  5. configs configs Public

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

    Nextflow 112 374

  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
  • atacseq Public

    ATAC-seq peak-calling and QC analysis pipeline

    nf-core/atacseq's past year of commit activity
    Nextflow 230 MIT 144 54 7 Updated Sep 29, 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 1,104 306 (1 issue needs help) 173 Updated Sep 29, 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 607 MIT 555 261 (5 issues need help) 41 Updated Sep 29, 2026
  • variantbenchmarking Public

    Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

    nf-core/variantbenchmarking's past year of commit activity
    Nextflow 51 MIT 31 28 (3 issues need help) 1 Updated Sep 29, 2026
  • moleculardynamics Public
    nf-core/moleculardynamics's past year of commit activity
    Nextflow 3 MIT 1 0 0 Updated Sep 29, 2026
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    nf-core/hadge's past year of commit activity
    Nextflow 26 MIT 10 11 1 Updated Sep 29, 2026
  • nft-utils Public

    nf-test utility functions

    nf-core/nft-utils's past year of commit activity
    Java 13 MIT 11 14 2 Updated Sep 29, 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 898 22 5 Updated Sep 29, 2026
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq's past year of commit activity
    Nextflow 262 MIT 158 15 0 Updated Sep 29, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag's past year of commit activity
    Nextflow 323 MIT 158 78 (1 issue needs help) 7 Updated Sep 29, 2026
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