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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 324 255

  2. modules modules Public

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

    Nextflow 430 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 899

  4. sarek sarek Public

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

    Nextflow 609 555

  5. configs configs Public

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

    Nextflow 113 374

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 201 repositories
  • rnaseq Public

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

    nf-core/rnaseq's past year of commit activity
    Nextflow 1,378 MIT 899 23 5 Updated Sep 30, 2026
  • pathogenepidemiology Public

    [DEVELOPMENT UNDERWAY] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

    nf-core/pathogenepidemiology's past year of commit activity
    Nextflow 3 MIT 2 12 (2 issues need help) 1 Updated Sep 30, 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
    163 MIT 536 43 33 Updated Sep 30, 2026
  • 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 7 1 Updated Sep 30, 2026
  • modules Public

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

    nf-core/modules's past year of commit activity
    Nextflow 430 MIT 1,108 306 (1 issue needs help) 174 Updated Sep 30, 2026
  • taxmarker Public

    Identify taxonomically mislabelled sequences

    nf-core/taxmarker's past year of commit activity
    Nextflow 1 MIT 1 9 0 Updated Sep 30, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 98 MIT 299 123 25 Updated Sep 30, 2026
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease's past year of commit activity
    Nextflow 126 MIT 70 17 5 Updated Sep 30, 2026
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies's past year of commit activity
    Nextflow 23 MIT 4 12 1 Updated Sep 30, 2026
  • viralrecon Public

    Assembly and intrahost/low-frequency variant calling for viral samples

    nf-core/viralrecon's past year of commit activity
    Nextflow 166 MIT 158 58 (4 issues need help) 4 Updated Sep 30, 2026
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