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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 246 193

  2. modules modules Public

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

    Nextflow 291 749

  3. rnaseq rnaseq Public

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

    Nextflow 971 717

  4. sarek sarek Public

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

    Nextflow 419 424

  5. chipseq chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 203 149

  6. eager eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Nextflow 156 82

Repositories

Showing 10 of 152 repositories
  • eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    nf-core/eager’s past year of commit activity
    Nextflow 156 MIT 82 38 (2 issues need help) 8 Updated Jan 31, 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 291 MIT 749 460 (1 issue needs help) 184 Updated Jan 31, 2025
  • riboseq Public

    Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

    nf-core/riboseq’s past year of commit activity
    Nextflow 12 MIT 8 15 2 Updated Jan 31, 2025
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 14 MIT 9 16 (1 issue needs help) 2 Updated Jan 31, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 209 90 34 Updated Jan 31, 2025
  • references-assets Public
    nf-core/references-assets’s past year of commit activity
    Shell 0 MIT 1 0 0 Updated Jan 31, 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 12 0 Updated Jan 31, 2025
  • pangenome Public

    Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

    nf-core/pangenome’s past year of commit activity
    Nextflow 80 MIT 18 9 1 Updated Jan 31, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 14 MIT 6 8 5 Updated Jan 31, 2025
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 93 MIT 284 12 16 Updated Jan 31, 2025
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