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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 297 235

  2. modules modules Public

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

    Nextflow 408 1k

  3. rnaseq rnaseq Public

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

    Nextflow 1.2k 858

  4. sarek sarek Public

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

    Nextflow 555 525

  5. configs configs Public

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

    Nextflow 108 351

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 188 repositories
  • 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
    157 MIT 488 38 25 Updated Apr 6, 2026
  • phaseimpute Public

    A bioinformatics pipeline to phase and impute genetic data

    nf-core/phaseimpute’s past year of commit activity
    Nextflow 30 MIT 20 8 1 Updated Apr 6, 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 408 MIT 1,033 329 (76 issues need help) 195 Updated Apr 6, 2026
  • diseasemodulediscovery Public

    A pipeline for network-based disease module identification.

    nf-core/diseasemodulediscovery’s past year of commit activity
    Python 5 MIT 4 37 7 Updated Apr 6, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 88 MIT 284 116 30 Updated Apr 6, 2026
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 3 3 37 24 Updated Apr 6, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 285 MIT 148 79 (1 issue needs help) 8 Updated Apr 6, 2026
  • isoseq Public

    Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

    nf-core/isoseq’s past year of commit activity
    Nextflow 49 MIT 20 9 2 Updated Apr 6, 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 34 MIT 17 21 (1 issue needs help) 0 Updated Apr 6, 2026
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 297 MIT 235 328 58 Updated Apr 6, 2026
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