Skip to content
@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

Pinned Loading

  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

Repositories

Showing 10 of 154 repositories
  • 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 38 Updated Feb 24, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 247 MIT 193 277 38 Updated Feb 24, 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 3 Updated Feb 24, 2025
  • 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 14 MIT 9 16 0 Updated Feb 24, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar’s past year of commit activity
    Nextflow 42 MIT 36 29 3 Updated Feb 24, 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 1 Updated Feb 24, 2025
  • metatdenovo Public

    Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

    nf-core/metatdenovo’s past year of commit activity
    Nextflow 23 MIT 11 5 1 Updated Feb 24, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 59 MIT 15 16 2 Updated Feb 24, 2025
  • genomeassembler Public
    nf-core/genomeassembler’s past year of commit activity
    Nextflow 17 MIT 13 1 2 Updated Feb 24, 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 20 1 Updated Feb 24, 2025
View all repositories