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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 256 201

  2. modules modules Public

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

    Nextflow 352 836

  3. rnaseq rnaseq Public

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

    Nextflow 1k 749

  4. sarek sarek Public

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

    Nextflow 439 440

  5. configs configs Public

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

    Nextflow 98 302

  6. proposals proposals Public

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

    6

Repositories

Showing 10 of 158 repositories
  • hlatyping Public

    Precision HLA typing from next-generation sequencing data

    nf-core/hlatyping’s past year of commit activity
    Nextflow 65 MIT 31 13 1 Updated Apr 14, 2025
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream’s past year of commit activity
    Nextflow 54 MIT 24 30 (3 issues need help) 4 Updated Apr 14, 2025
  • spatialxe Public
    nf-core/spatialxe’s past year of commit activity
    Nextflow 15 MIT 7 30 2 Updated Apr 14, 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 352 MIT 836 513 (1 issue needs help) 177 Updated Apr 14, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 99 MIT 44 36 4 Updated Apr 14, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 75 MIT 245 94 26 Updated Apr 14, 2025
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    3 MIT 1 0 2 Updated Apr 14, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 17 MIT 6 5 6 Updated Apr 14, 2025
  • methylseq Public

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

    nf-core/methylseq’s past year of commit activity
    Nextflow 165 MIT 153 26 (1 issue needs help) 9 Updated Apr 14, 2025
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 9 MIT 5 1 3 Updated Apr 14, 2025
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