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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 328 267

  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 909

  4. sarek sarek Public

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

    Nextflow 614 565

  5. configs configs Public

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

    Nextflow 114 377

  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
  • rangeland Public

    Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.

    nf-core/rangeland's past year of commit activity
    Nextflow 11 MIT 5 5 3 Updated Oct 27, 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 1,130 281 (1 issue needs help) 191 Updated Oct 27, 2026
  • rnasplice Public

    rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

    nf-core/rnasplice's past year of commit activity
    Nextflow 70 MIT 43 6 1 Updated Oct 27, 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 118 MIT 70 11 3 Updated Oct 27, 2026
  • captnseq Public

    CAPTn-seq is an extended Tn-seq pipeline that goes 1) from raw reads to gene essentiality then 2) to gene-gene interaction calls (from HTTM experiments).

    nf-core/captnseq's past year of commit activity
    Nextflow 0 MIT 1 6 0 Updated Oct 27, 2026
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery's past year of commit activity
    Nextflow 6 MIT 6 38 13 Updated Oct 27, 2026
  • metaboigniter Public

    Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.

    nf-core/metaboigniter's past year of commit activity
    Nextflow 24 MIT 19 17 6 Updated Oct 27, 2026
  • viralmetagenome Public

    A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

    nf-core/viralmetagenome's past year of commit activity
    Nextflow 42 MIT 14 16 (1 issue needs help) 2 Updated Oct 27, 2026
  • taxmarker Public

    Identify taxonomically mislabelled sequences

    nf-core/taxmarker's past year of commit activity
    Nextflow 2 MIT 3 10 0 Updated Oct 27, 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 1 Updated Oct 27, 2026
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