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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 324 259

  2. modules modules Public

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

    Nextflow 431 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 903

  4. sarek sarek Public

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

    Nextflow 612 558

  5. configs configs Public

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

    Nextflow 113 376

  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
  • datasync Public

    nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks

    nf-core/datasync's past year of commit activity
    Nextflow 11 MIT 8 6 1 Updated Oct 6, 2026
  • 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 1,379 MIT 903 24 6 Updated Oct 6, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 98 MIT 299 121 24 Updated Oct 6, 2026
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa's past year of commit activity
    Nextflow 21 MIT 8 3 1 Updated Oct 6, 2026
  • bamtofastq Public

    Converts bam or cram files to fastq format and does quality control.

    nf-core/bamtofastq's past year of commit activity
    Nextflow 32 MIT 17 8 2 Updated Oct 6, 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 431 MIT 1,110 296 (1 issue needs help) 173 Updated Oct 6, 2026
  • demo Public

    nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

    nf-core/demo's past year of commit activity
    Nextflow 16 MIT 28 3 5 Updated Oct 6, 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 6 Updated Oct 6, 2026
  • deepmutscan Public

    nf-core/deepmutscan is a reproducible, scalable, and community-curated pipeline for analyzing deep mutational scanning (DMS) data using shotgun DNA sequencing.

    nf-core/deepmutscan's past year of commit activity
    Nextflow 5 MIT 5 7 6 Updated Oct 6, 2026
  • rnastructurome Public

    a bioinformatics pipeline for analysing chemical high-throughput RNA structure-probing data

    nf-core/rnastructurome's past year of commit activity
    Nextflow 8 MIT 2 0 0 Updated Oct 6, 2026
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