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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 283 221

  2. modules modules Public

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

    Nextflow 388 942

  3. rnaseq rnaseq Public

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

    Nextflow 1.2k 823

  4. sarek sarek Public

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

    Nextflow 506 491

  5. configs configs Public

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

    Nextflow 104 338

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 177 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 388 MIT 942 394 (1 issue needs help) 169 Updated Dec 8, 2025
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 112 MIT 55 47 5 Updated Dec 8, 2025
  • 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 24 MIT 5 8 3 Updated Dec 8, 2025
  • metapep Public

    From metagenomes to epitopes and beyond

    nf-core/metapep’s past year of commit activity
    Nextflow 12 MIT 8 15 3 Updated Dec 8, 2025
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    Nextflow 19 MIT 4 2 1 Updated Dec 8, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 81 MIT 254 111 23 Updated Dec 8, 2025
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies’s past year of commit activity
    Nextflow 21 MIT 3 9 1 Updated Dec 8, 2025
  • 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
    144 MIT 449 35 17 Updated Dec 8, 2025
  • 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 506 MIT 490 307 (6 issues need help) 39 Updated Dec 8, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 283 MIT 221 322 42 Updated Dec 8, 2025
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