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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 321 254

  2. modules modules Public

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

    Nextflow 428 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 896

  4. sarek sarek Public

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

    Nextflow 602 548

  5. configs configs Public

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

    Nextflow 112 375

  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
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 98 MIT 298 121 19 Updated Sep 18, 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 Sep 18, 2026
  • pathogenepidemiology Public

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

    nf-core/pathogenepidemiology's past year of commit activity
    Nextflow 3 MIT 2 10 0 Updated Sep 17, 2026
  • funcprofiler Public

    Read-based functional profiling of microbiome sequencing data

    nf-core/funcprofiler's past year of commit activity
    Nextflow 3 MIT 5 12 4 Updated Sep 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 428 MIT 1,098 316 (1 issue needs help) 176 Updated Sep 17, 2026
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar's past year of commit activity
    Nextflow 61 MIT 47 22 5 Updated Sep 18, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream's past year of commit activity
    Nextflow 115 MIT 66 24 (2 issues need help) 2 Updated Sep 18, 2026
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq's past year of commit activity
    Nextflow 259 MIT 156 24 6 Updated Sep 17, 2026
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    nf-core/test-datasets's past year of commit activity
    164 MIT 529 43 35 Updated Sep 17, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag's past year of commit activity
    Nextflow 320 MIT 156 77 (1 issue needs help) 7 Updated Sep 17, 2026
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