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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 247 193

  2. modules modules Public

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

    Nextflow 292 752

  3. rnaseq rnaseq Public

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

    Nextflow 986 721

  4. sarek sarek Public

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

    Nextflow 424 428

  5. chipseq chipseq Public

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

    Nextflow 206 149

  6. eager eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Nextflow 159 81

Repositories

Showing 10 of 154 repositories
  • methylarray Public

    Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.

    nf-core/methylarray’s past year of commit activity
    Nextflow 3 MIT 1 0 1 Updated Feb 23, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 33 8 Updated Feb 23, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar’s past year of commit activity
    Nextflow 42 MIT 36 33 4 Updated Feb 23, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 219 90 41 Updated Feb 23, 2025
  • molkart Public

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

    nf-core/molkart’s past year of commit activity
    Nextflow 11 MIT 9 13 1 Updated Feb 21, 2025
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 95 MIT 289 12 15 Updated Feb 21, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 94 MIT 38 34 2 Updated Feb 21, 2025
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval’s past year of commit activity
    Nextflow 6 MIT 2 3 0 Updated Feb 21, 2025
  • multiplesequencealign Public

    A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

    nf-core/multiplesequencealign’s past year of commit activity
    Nextflow 27 MIT 12 5 0 Updated Feb 21, 2025
  • phyloplace Public

    nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

    nf-core/phyloplace’s past year of commit activity
    Nextflow 9 MIT 4 1 0 Updated Feb 21, 2025
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