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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 283 221

  2. modules modules Public

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

    Nextflow 388 943

  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 824

  4. sarek sarek Public

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

    Nextflow 506 492

  5. configs configs Public

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

    Nextflow 104 338

  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
  • 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 10 MIT 5 6 1 Updated Dec 9, 2025
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

    nf-core/methylseq’s past year of commit activity
    Nextflow 182 MIT 161 13 4 Updated Dec 9, 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 388 MIT 943 395 (1 issue needs help) 170 Updated Dec 9, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 254 111 24 Updated Dec 9, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 97 MIT 26 11 7 Updated Dec 9, 2025
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease’s past year of commit activity
    Nextflow 112 MIT 55 47 4 Updated Dec 8, 2025
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 21 MIT 3 9 0 Updated Dec 8, 2025
  • 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 13 14 4 Updated Dec 8, 2025
  • rnadnavar Public

    Pipeline for RNA and DNA integrated analysis for somatic mutation detection

    nf-core/rnadnavar’s past year of commit activity
    Nextflow 11 MIT 9 3 4 Updated Dec 8, 2025
  • metapep Public

    From metagenomes to epitopes and beyond

    nf-core/metapep’s past year of commit activity
    Nextflow 12 MIT 8 15 4 Updated Dec 8, 2025
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