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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 331 269

  2. modules modules Public

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

    Nextflow 438 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 911

  4. sarek sarek Public

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

    Nextflow 622 565

  5. configs configs Public

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

    Nextflow 114 380

  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
  • 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 622 MIT 565 228 (5 issues need help) 39 Updated Nov 13, 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 438 MIT 1,144 300 (1 issue needs help) 169 Updated Nov 13, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream's past year of commit activity
    Nextflow 118 MIT 72 10 2 Updated Nov 13, 2026
  • magmap Public

    Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

    nf-core/magmap's past year of commit activity
    Nextflow 13 MIT 7 17 1 Updated Nov 13, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 100 MIT 300 126 28 Updated Nov 13, 2026
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq's past year of commit activity
    Nextflow 104 MIT 140 22 (2 issues need help) 1 Updated Nov 13, 2026
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 331 MIT 269 374 88 Updated Nov 13, 2026
  • phaseimpute Public

    A bioinformatics pipeline to phase and impute genetic data

    nf-core/phaseimpute's past year of commit activity
    Nextflow 36 MIT 23 9 2 Updated Nov 13, 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 380 13 31 Updated Nov 13, 2026
  • nf-core-utils Public

    Nextflow plugin with nf-core utility functions

    nf-core/nf-core-utils's past year of commit activity
    Groovy 1 Apache-2.0 4 22 10 Updated Nov 13, 2026
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