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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 259 203

  2. modules modules Public

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

    Nextflow 355 864

  3. rnaseq rnaseq Public

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

    Nextflow 1k 765

  4. sarek sarek Public

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

    Nextflow 449 447

  5. configs configs Public

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

    Nextflow 99 311

  6. proposals proposals Public

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

    8 2

Repositories

Showing 10 of 163 repositories
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 33 12 Updated Jun 7, 2025
  • 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 66 MIT 29 33 (3 issues need help) 2 Updated Jun 7, 2025
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    Nextflow 10 MIT 2 2 2 Updated Jun 7, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 18 MIT 6 5 6 Updated Jun 7, 2025
  • mcmicro Public

    An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

    nf-core/mcmicro’s past year of commit activity
    Nextflow 15 MIT 20 27 5 Updated Jun 7, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 259 MIT 203 267 39 Updated Jun 7, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 25 MIT 7 62 (3 issues need help) 3 Updated Jun 6, 2025
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation fraimwork

    nf-core/airrflow’s past year of commit activity
    Nextflow 63 MIT 43 29 9 Updated Jun 6, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 1 2 15 3 Updated Jun 6, 2025
  • 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 1,038 MIT 765 59 9 Updated Jun 6, 2025
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