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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 322 255

  2. modules modules Public

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

    Nextflow 429 1.1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.4k 897

  4. sarek sarek Public

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

    Nextflow 604 550

  5. configs configs Public

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

    Nextflow 112 374

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 201 repositories
  • references Public

    nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

    nf-core/references's past year of commit activity
    Nextflow 23 MIT 6 26 1 Updated Sep 23, 2026
  • metatdenovo Public

    Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

    nf-core/metatdenovo's past year of commit activity
    Nextflow 36 MIT 21 18 1 Updated Sep 23, 2026
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq's past year of commit activity
    Nextflow 261 MIT 157 25 4 Updated Sep 23, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 98 MIT 298 121 18 Updated Sep 23, 2026
  • rnasplice Public

    rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

    nf-core/rnasplice's past year of commit activity
    Nextflow 69 MIT 40 6 1 Updated Sep 23, 2026
  • modules Public

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

    nf-core/modules's past year of commit activity
    Nextflow 429 MIT 1,098 299 (1 issue needs help) 170 Updated Sep 23, 2026
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies's past year of commit activity
    Nextflow 23 MIT 4 12 0 Updated Sep 23, 2026
  • phyloplace Public

    nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

    nf-core/phyloplace's past year of commit activity
    Nextflow 12 MIT 4 1 0 Updated Sep 23, 2026
  • 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 1,371 MIT 897 13 3 Updated Sep 23, 2026
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 322 MIT 255 358 82 Updated Sep 23, 2026
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