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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 Public

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

    Python 257 203

  2. modules Public

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

    Nextflow 355 857

  3. rnaseq Public

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

    Nextflow 1k 756

  4. sarek Public

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

    Nextflow 442 444

  5. configs Public

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

    Nextflow 99 309

  6. proposals Public

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

    8 1

Repositories

Showing 10 of 161 repositories
  • multiplesequencealign Public

    A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

    Nextflow 32 MIT 14 6 2 Updated May 17, 2025
  • website Public

    Code and files for the main nf-core website.

    MDX 76 MIT 246 94 32 Updated May 17, 2025
  • ops Public
    Python 2 2 31 10 Updated May 17, 2025
  • circrna Public

    circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

    Nextflow 54 MIT 30 17 3 Updated May 17, 2025
  • proteinfamilies Public

    Generation and update of protein families

    Nextflow 14 MIT 2 12 2 Updated May 17, 2025
  • stats Public
    HTML 1 2 13 3 Updated May 17, 2025
  • fetchngs Public

    Pipeline to fetch metadata and raw FastQ files from public databases

    Nextflow 175 MIT 81 32 11 Updated May 16, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    TypeScript 18 MIT 6 5 6 Updated May 16, 2025
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    Nextflow 74 MIT 60 32 (1 issue needs help) 7 Updated May 16, 2025
  • nf-utils Public

    Nextflow plugin for nf-core utils

    Groovy 1 Apache-2.0 0 3 0 Updated May 16, 2025
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