Skip to content
@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

Pinned Loading

  1. tools tools Public

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

    Python 327 266

  2. modules modules Public

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

    Nextflow 433 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 909

  4. sarek sarek Public

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

    Nextflow 614 563

  5. configs configs Public

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

    Nextflow 114 377

  6. proposals proposals Public

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

    10 6

Repositories

Showing 10 of 203 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 25 0 Updated Oct 23, 2026
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 327 MIT 266 371 97 Updated Oct 23, 2026
  • website Public

    Code and files for the main nf-core website.

    nf-core/website's past year of commit activity
    MDX 99 MIT 301 125 34 Updated Oct 23, 2026
  • seqsubmit Public

    nf-core pipeline for data submission to ENA

    nf-core/seqsubmit's past year of commit activity
    Nextflow 22 MIT 11 21 6 Updated Oct 23, 2026
  • nf-core-utils Public

    Nextflow plugin with nf-core utility functions

    nf-core/nf-core-utils's past year of commit activity
    Groovy 1 Apache-2.0 1 20 9 Updated Oct 23, 2026
  • fastqrepair Public

    A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered

    nf-core/fastqrepair's past year of commit activity
    Nextflow 9 MIT 6 16 2 Updated Oct 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 433 MIT 1,127 288 (1 issue needs help) 192 Updated Oct 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 37 MIT 22 50 4 Updated Oct 23, 2026
  • taxmarker Public

    Identify taxonomically mislabelled sequences

    nf-core/taxmarker's past year of commit activity
    Nextflow 2 MIT 3 11 (1 issue needs help) 3 Updated Oct 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 70 MIT 43 5 0 Updated Oct 23, 2026
View all repositories

Most used topics

Loading…