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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 273 214

  2. modules modules Public

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

    Nextflow 379 911

  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 802

  4. sarek sarek Public

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

    Nextflow 491 483

  5. configs configs Public

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

    Nextflow 104 332

  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
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery’s past year of commit activity
    Python 5 MIT 3 32 6 Updated Oct 17, 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 24 MIT 20 29 5 Updated Oct 17, 2025
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    nf-core/airrflow’s past year of commit activity
    Nextflow 66 MIT 45 34 5 Updated Oct 17, 2025
  • bamtofastq Public

    Converts bam or cram files to fastq format and does quality control.

    nf-core/bamtofastq’s past year of commit activity
    Nextflow 30 MIT 18 5 1 Updated Oct 17, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 80 MIT 249 102 24 Updated Oct 17, 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 Oct 17, 2025
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 10 MIT 1 1 2 Updated Oct 17, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 249 MIT 141 66 (1 issue needs help) 9 Updated Oct 17, 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 379 MIT 911 370 (1 issue needs help) 151 Updated Oct 17, 2025
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 21 MIT 3 8 0 Updated Oct 17, 2025
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