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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 257 203

  2. modules modules Public

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

    Nextflow 355 856

  3. rnaseq rnaseq Public

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

    Nextflow 1k 756

  4. sarek sarek Public

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

    Nextflow 442 444

  5. configs configs Public

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

    Nextflow 99 309

  6. proposals proposals Public

    Where new ideas for nf-core pipelines, special interest groups and more are proposed

    8 1

Repositories

Showing 10 of 161 repositories
  • proteinfamilies Public

    Generation and update of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 14 MIT 2 12 1 Updated May 15, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 159 MIT 112 25 (5 issues need help) 2 Updated May 15, 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 355 MIT 856 465 (1 issue needs help) 181 Updated May 15, 2025
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    Nextflow 80 MIT 57 38 (2 issues need help) 4 Updated May 15, 2025
  • genomeassembler Public

    Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads

    nf-core/genomeassembler’s past year of commit activity
    Nextflow 24 MIT 16 3 1 Updated May 15, 2025
  • nanoseq Public

    Nanopore demultiplexing, QC and alignment pipeline

    nf-core/nanoseq’s past year of commit activity
    Nextflow 201 MIT 95 50 2 Updated May 15, 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 29 MIT 14 22 0 Updated May 15, 2025
  • 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 4 MIT 3 12 3 Updated May 15, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 18 MIT 6 5 6 Updated May 15, 2025
  • scnanoseq Public

    Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

    nf-core/scnanoseq’s past year of commit activity
    Nextflow 35 MIT 14 14 5 Updated May 15, 2025
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