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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 269 210

  2. modules modules Public

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

    Nextflow 377 907

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 798

  4. sarek sarek Public

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

    Nextflow 483 477

  5. configs configs Public

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

    Nextflow 103 328

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 171 repositories
  • tfactivity Public

    Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

    nf-core/tfactivity’s past year of commit activity
    Nextflow 12 MIT 5 0 1 Updated Sep 26, 2025
  • mcmicro Public

    An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

    nf-core/mcmicro’s past year of commit activity
    Nextflow 22 MIT 20 30 4 Updated Sep 26, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 78 MIT 247 100 21 Updated Sep 26, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 377 MIT 907 382 (1 issue needs help) 167 Updated Sep 26, 2025
  • sammyseq Public

    Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

    nf-core/sammyseq’s past year of commit activity
    Nextflow 5 MIT 16 5 (1 issue needs help) 0 Updated Sep 26, 2025
  • magmap Public

    Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

    nf-core/magmap’s past year of commit activity
    Nextflow 7 MIT 4 2 2 Updated Sep 26, 2025
  • metapep Public

    From metagenomes to epitopes and beyond

    nf-core/metapep’s past year of commit activity
    Nextflow 12 MIT 10 14 4 Updated Sep 26, 2025
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 19 MIT 3 3 0 Updated Sep 26, 2025
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 2 34 13 Updated Sep 26, 2025
  • proposals Public

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

    nf-core/proposals’s past year of commit activity
    8 MIT 3 20 4 Updated Sep 26, 2025
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