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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 250 197

  2. modules modules Public

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

    Nextflow 295 755

  3. rnaseq rnaseq Public

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

    Nextflow 993 732

  4. sarek sarek Public

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

    Nextflow 430 432

Repositories

Showing 10 of 155 repositories
  • 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 95 MIT 293 8 10 Updated Mar 15, 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
    117 MIT 369 31 9 Updated Mar 15, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 72 MIT 233 92 35 Updated Mar 15, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 2 14 11 Updated Mar 15, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 150 MIT 105 47 (5 issues need help) 6 Updated Mar 14, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 295 MIT 755 477 (1 issue needs help) 118 Updated Mar 14, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 40 9 Updated Mar 14, 2025
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    nf-core/bacass’s past year of commit activity
    Nextflow 68 MIT 43 21 (1 issue needs help) 1 Updated Mar 14, 2025
  • spatialvi Public

    Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

    nf-core/spatialvi’s past year of commit activity
    Nextflow 59 MIT 20 6 1 Updated Mar 14, 2025
  • eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    nf-core/eager’s past year of commit activity
    Nextflow 160 MIT 82 37 (2 issues need help) 8 Updated Mar 14, 2025
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