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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 252 200

  2. modules modules Public

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

    Nextflow 297 798

  3. rnaseq rnaseq Public

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

    Nextflow 1k 744

  4. sarek sarek Public

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

    Nextflow 432 436

Repositories

Showing 10 of 157 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 297 MIT 798 551 (1 issue needs help) 149 Updated Mar 25, 2025
  • methylseq Public

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

    nf-core/methylseq’s past year of commit activity
    Nextflow 160 MIT 152 27 (1 issue needs help) 8 Updated Mar 25, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 15 MIT 6 5 6 Updated Mar 25, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 74 MIT 242 95 31 Updated Mar 25, 2025
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 9 MIT 4 3 2 Updated Mar 25, 2025
  • pacvar Public

    Longread PacBio sequencing processing for WGS and PureTarget

    nf-core/pacvar’s past year of commit activity
    Nextflow 8 MIT 6 4 2 Updated Mar 24, 2025
  • clipseq Public

    CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

    nf-core/clipseq’s past year of commit activity
    Nextflow 21 MIT 37 33 5 Updated Mar 24, 2025
  • bactmap Public

    A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

    nf-core/bactmap’s past year of commit activity
    Nextflow 53 MIT 47 38 (1 issue needs help) 3 Updated Mar 24, 2025
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    nf-core/airrflow’s past year of commit activity
    Nextflow 58 MIT 40 22 4 Updated Mar 24, 2025
  • proteinannotator Public

    The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 1 MIT 1 8 1 Updated Mar 24, 2025
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