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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 327 265

  2. modules modules Public

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

    Nextflow 432 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 904

  4. sarek sarek Public

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

    Nextflow 614 562

  5. configs configs Public

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

    Nextflow 114 376

  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
  • 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 16, 2026
  • nf-core-utils Public

    Nextflow plugin with nf-core utility functions

    nf-core/nf-core-utils's past year of commit activity
    Groovy 1 Apache-2.0 1 24 9 Updated Oct 16, 2026
  • actions Public

    Centralised GitHub Actions for nf-core.

    nf-core/actions's past year of commit activity
    TypeScript 0 MIT 1 1 2 Updated Oct 16, 2026
  • seqsubmit Public

    nf-core pipeline for data submission to ENA

    nf-core/seqsubmit's past year of commit activity
    Nextflow 22 MIT 11 24 6 Updated Oct 16, 2026
  • variantbenchmarking Public

    Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

    nf-core/variantbenchmarking's past year of commit activity
    Nextflow 51 MIT 33 28 (3 issues need help) 4 Updated Oct 16, 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 432 MIT 1,123 293 (1 issue needs help) 194 Updated Oct 16, 2026
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies's past year of commit activity
    Nextflow 23 MIT 5 15 1 Updated Oct 16, 2026
  • chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    nf-core/chipseq's past year of commit activity
    Nextflow 245 MIT 184 17 6 Updated Oct 16, 2026
  • molkart Public

    A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

    nf-core/molkart's past year of commit activity
    Nextflow 14 MIT 12 10 4 Updated Oct 16, 2026
  • circrna Public

    circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

    nf-core/circrna's past year of commit activity
    Nextflow 61 MIT 33 17 1 Updated Oct 16, 2026
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