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 Public

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

    Python 252 201

  2. modules Public

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

    Nextflow 349 833

  3. rnaseq Public

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

    Nextflow 1k 746

  4. sarek Public

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

    Nextflow 436 438

  5. configs Public

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

    Nextflow 97 298

  6. proposals Public

    Where new ideas for nf-core pipelines and more are proposed

    3

Repositories

Showing 10 of 158 repositories
  • modules Public

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

    Nextflow 349 MIT 833 522 (1 issue needs help) 169 Updated Apr 1, 2025
  • stats Public
    HTML 0 2 13 9 Updated Apr 1, 2025
  • dualrnaseq Public

    Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

    Nextflow 21 MIT 35 19 8 Updated Apr 1, 2025
  • airrflow Public

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

    Nextflow 58 MIT 40 23 3 Updated Apr 1, 2025
  • proteinannotator Public

    The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations

    Nextflow 1 MIT 3 10 4 Updated Apr 1, 2025
  • sarek Public

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

    Nextflow 436 MIT 438 274 (6 issues need help) 40 Updated Apr 1, 2025
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    120 MIT 389 33 11 Updated Apr 1, 2025
  • website Public

    Code and files for the main nf-core website.

    MDX 74 MIT 245 95 25 Updated Apr 1, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    Nextflow 45 MIT 37 9 1 Updated Apr 1, 2025
  • genomeqc Public

    Compare the quality of multiple genomes, along with their annotations.

    Nextflow 8 MIT 16 40 (2 issues need help) 6 Updated Apr 1, 2025
View all repositories