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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 292 224

  2. modules modules Public

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

    Nextflow 398 967

  3. rnaseq rnaseq Public

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    Nextflow 1.2k 847

  4. sarek sarek Public

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

    Nextflow 546 522

  5. configs configs Public

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

    Nextflow 107 340

  6. proposals proposals Public

    Where new ideas for nf-core pipelines, special interest groups and more are proposed

    8 4

Repositories

Showing 10 of 182 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 398 MIT 967 381 (1 issue needs help) 166 Updated Feb 17, 2026
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 178 MIT 61 45 (1 issue needs help) 6 Updated Feb 17, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 273 MIT 146 79 (1 issue needs help) 8 Updated Feb 17, 2026
  • ops Public

    Different *Ops related scripts for the nf-core org.

    nf-core/ops’s past year of commit activity
    Python 3 2 37 22 Updated Feb 17, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 85 MIT 267 115 35 Updated Feb 17, 2026
  • cutandrun Public

    Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

    nf-core/cutandrun’s past year of commit activity
    Nextflow 107 MIT 68 45 8 Updated Feb 17, 2026
  • hackathon-infra Public

    Terraform infrastructure for nf-core hackathon virtual events

    nf-core/hackathon-infra’s past year of commit activity
    Shell 0 MIT 0 0 1 Updated Feb 17, 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 546 MIT 522 238 (5 issues need help) 36 Updated Feb 17, 2026
  • logos Public

    Host nf-core logos and templates for making new logos

    nf-core/logos’s past year of commit activity
    7 MIT 15 0 0 Updated Feb 17, 2026
  • cageseq Public

    CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

    nf-core/cageseq’s past year of commit activity
    Nextflow 11 MIT 12 3 6 Updated Feb 17, 2026
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