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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 330 268

  2. modules modules Public

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

    Nextflow 436 1.1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.4k 910

  4. sarek sarek Public

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

    Nextflow 617 565

  5. configs configs Public

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

    Nextflow 114 377

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 203 repositories
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval's past year of commit activity
    Nextflow 30 MIT 11 4 2 Updated Nov 6, 2026
  • seqsubmit Public

    nf-core pipeline for data submission to ENA

    nf-core/seqsubmit's past year of commit activity
    Nextflow 22 MIT 11 16 3 Updated Nov 6, 2026
  • 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 114 MIT 377 14 31 Updated Nov 6, 2026
  • 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 26 MIT 43 48 10 Updated Nov 6, 2026
  • funcscan Public

    (Meta-)genome screening for functional and natural product gene sequences

    nf-core/funcscan's past year of commit activity
    Nextflow 119 MIT 42 19 4 Updated Nov 6, 2026
  • sarek Public

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

    nf-core/sarek's past year of commit activity
    Nextflow 617 MIT 565 232 (5 issues need help) 50 Updated Nov 6, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 100 MIT 300 125 28 Updated Nov 6, 2026
  • genomeqc Public

    Compare the quality of multiple genomes, along with their annotations.

    nf-core/genomeqc's past year of commit activity
    Nextflow 26 MIT 24 22 2 Updated Nov 6, 2026
  • genephylo Public
    nf-core/genephylo's past year of commit activity
    Nextflow 0 MIT 1 3 0 Updated Nov 6, 2026
  • test-datasets Public

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

    nf-core/test-datasets's past year of commit activity
    165 MIT 549 43 40 Updated Nov 6, 2026
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