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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 283 223

  2. modules modules Public

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

    Nextflow 389 949

  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 828

  4. sarek sarek Public

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

    Nextflow 529 497

  5. configs configs Public

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

    Nextflow 105 339

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 177 repositories
  • riboseq Public

    Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

    nf-core/riboseq’s past year of commit activity
    Nextflow 18 MIT 15 13 5 Updated Dec 19, 2025
  • rnaseq Public

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

    nf-core/rnaseq’s past year of commit activity
    Nextflow 1,172 MIT 828 33 11 Updated Dec 19, 2025
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    Nextflow 19 MIT 6 2 1 Updated Dec 19, 2025
  • lsmquant Public

    A pipeline for processing and analysis of light-sheet microscopy images.

    nf-core/lsmquant’s past year of commit activity
    Nextflow 5 MIT 1 0 4 Updated Dec 19, 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 389 MIT 949 392 (1 issue needs help) 164 Updated Dec 19, 2025
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery’s past year of commit activity
    Python 5 MIT 3 36 6 Updated Dec 19, 2025
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 11 MIT 1 1 3 Updated Dec 19, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 168 MIT 120 16 (1 issue needs help) 5 Updated Dec 19, 2025
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 21 MIT 3 7 0 Updated Dec 19, 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 15 5 1 Updated Dec 19, 2025
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