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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 252 201

  2. modules modules Public

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

    Nextflow 350 833

  3. rnaseq rnaseq Public

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

    Nextflow 1k 747

  4. sarek sarek Public

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

    Nextflow 436 439

  5. configs configs Public

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

    Nextflow 97 298

  6. proposals proposals Public

    Where new ideas for nf-core pipelines and more are proposed

    3

Repositories

Showing 10 of 158 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 74 MIT 245 95 26 Updated Apr 3, 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 350 MIT 833 524 (1 issue needs help) 166 Updated Apr 3, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 40 10 Updated Apr 3, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar’s past year of commit activity
    Nextflow 45 MIT 37 9 1 Updated Apr 3, 2025
  • epitopeprediction Public

    A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

    nf-core/epitopeprediction’s past year of commit activity
    Nextflow 42 MIT 24 21 1 Updated Apr 3, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 151 MIT 108 49 (5 issues need help) 5 Updated Apr 3, 2025
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 76 MIT 45 62 (1 issue needs help) 6 Updated Apr 3, 2025
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 9 MIT 5 1 2 Updated Apr 3, 2025
  • tools Public

    Python package with helper tools for the nf-core community.

    nf-core/tools’s past year of commit activity
    Python 252 MIT 201 267 32 Updated Apr 3, 2025
  • spatialvi Public

    Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

    nf-core/spatialvi’s past year of commit activity
    Nextflow 60 MIT 22 6 2 Updated Apr 3, 2025
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