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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 286 224

  2. modules modules Public

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

    Nextflow 393 955

  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 840

  4. sarek sarek Public

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

    Nextflow 538 517

  5. configs configs Public

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

    Nextflow 107 339

  6. proposals proposals Public

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

    8 4

Repositories

Showing 10 of 180 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 393 MIT 955 378 (1 issue needs help) 173 Updated Jan 26, 2026
  • nanostring Public

    An analysis pipeline for Nanostring nCounter expression data.

    nf-core/nanostring’s past year of commit activity
    Nextflow 16 MIT 12 4 1 Updated Jan 26, 2026
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 269 MIT 145 73 (1 issue needs help) 8 Updated Jan 26, 2026
  • 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 538 MIT 517 304 (5 issues need help) 40 Updated Jan 26, 2026
  • pairgenomealign Public

    Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

    nf-core/pairgenomealign’s past year of commit activity
    Nextflow 10 MIT 4 20 1 Updated Jan 26, 2026
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 286 MIT 224 327 48 Updated Jan 26, 2026
  • proteinannotator Public

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

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 9 MIT 8 21 5 Updated Jan 26, 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 1,188 MIT 840 38 12 Updated Jan 26, 2026
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease’s past year of commit activity
    Nextflow 112 MIT 56 49 5 Updated Jan 26, 2026
  • demo Public

    nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

    nf-core/demo’s past year of commit activity
    Nextflow 10 MIT 21 2 2 Updated Jan 26, 2026
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