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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 Public

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

    Python 252 200

  2. modules Public

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

    Nextflow 328 817

  3. 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 Public

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

    Nextflow 432 437

Repositories

Showing 10 of 158 repositories
  • coproid Public

    Coprolite host Identification pipeline

    Nextflow 9 MIT 5 2 3 Updated Mar 26, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    Nextflow 62 MIT 16 24 3 Updated Mar 25, 2025
  • modules Public

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

    Nextflow 328 MIT 817 560 (1 issue needs help) 173 Updated Mar 25, 2025
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    118 MIT 378 32 10 Updated Mar 26, 2025
  • nanostring Public

    An analysis pipeline for Nanostring nCounter expression data.

    Nextflow 13 MIT 11 6 1 Updated Mar 26, 2025
  • ops Public
    Python 1 2 40 9 Updated Mar 25, 2025
  • proteinannotator Public

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

    Nextflow 1 MIT 1 9 2 Updated Mar 25, 2025
  • clipseq Public

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

    Nextflow 21 MIT 40 34 7 Updated Mar 25, 2025
  • rnaseq Public

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

    Nextflow 1,002 MIT 744 82 16 Updated Mar 26, 2025
  • tfactivity Public

    Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

    Nextflow 10 MIT 4 1 1 Updated Mar 25, 2025
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