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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 260 204

  2. modules modules Public

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

    Nextflow 359 878

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 773

  4. sarek sarek Public

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

    Nextflow 453 450

  5. configs configs Public

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

    Nextflow 100 315

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 166 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 453 MIT 450 295 (6 issues need help) 41 Updated Jul 3, 2025
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 154 MIT 53 37 (1 issue needs help) 5 Updated Jul 3, 2025
  • 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 100 MIT 315 8 12 Updated Jul 3, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 245 88 13 Updated Jul 3, 2025
  • nf-core-utils Public

    Nextflow plugin for nf-core utils

    nf-core/nf-core-utils’s past year of commit activity
    Groovy 1 Apache-2.0 0 6 1 Updated Jul 3, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 159 MIT 112 32 (5 issues need help) 5 Updated Jul 3, 2025
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval’s past year of commit activity
    Nextflow 20 MIT 4 10 0 Updated Jul 3, 2025
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq’s past year of commit activity
    Nextflow 209 MIT 138 21 2 Updated Jul 3, 2025
  • reportho Public

    nf-core pipeline for comparative analysis of ortholog predictions

    nf-core/reportho’s past year of commit activity
    Nextflow 11 MIT 6 7 1 Updated Jul 3, 2025
  • panoramaseq Public

    a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays

    nf-core/panoramaseq’s past year of commit activity
    HTML 0 MIT 0 0 1 Updated Jul 3, 2025
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