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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 262 207

  2. modules modules Public

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

    Nextflow 364 883

  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 784

  4. sarek sarek Public

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

    Nextflow 461 459

  5. configs configs Public

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

    Nextflow 102 316

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 169 repositories
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 77 MIT 22 23 4 Updated Jul 25, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 75 MIT 245 88 12 Updated Jul 24, 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 364 MIT 883 429 (1 issue needs help) 173 Updated Jul 24, 2025
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

    nf-core/methylseq’s past year of commit activity
    Nextflow 168 MIT 157 24 (1 issue needs help) 7 Updated Jul 24, 2025
  • airrflow Public

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

    nf-core/airrflow’s past year of commit activity
    Nextflow 65 MIT 45 28 7 Updated Jul 24, 2025
  • fastquorum Public

    Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

    nf-core/fastquorum’s past year of commit activity
    Nextflow 23 MIT 16 11 (1 issue needs help) 1 Updated Jul 24, 2025
  • 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 461 MIT 459 293 (6 issues need help) 38 Updated Jul 24, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 262 MIT 207 276 35 Updated Jul 24, 2025
  • ops Public

    Different *Ops related scripts for the nf-core org.

    nf-core/ops’s past year of commit activity
    Python 3 2 34 8 Updated Jul 24, 2025
  • sopa Public

    Nextflow version of Sopa - spatial omics pipeline and analysis

    nf-core/sopa’s past year of commit activity
    Nextflow 4 MIT 1 0 1 Updated Jul 24, 2025
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