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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 328 267

  2. modules modules Public

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

    Nextflow 434 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 614 565

  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
  • genomicrelatedness Public

    Bioinformatics pipeline for estimating genetic relatedness from low-coverage whole-genome sequencing (sWGS) data

    nf-core/genomicrelatedness's past year of commit activity
    Nextflow 2 MIT 5 0 0 Updated Oct 26, 2026
  • tools Public

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

    nf-core/tools's past year of commit activity
    Python 328 MIT 267 369 97 Updated Oct 26, 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 434 MIT 1,130 286 (1 issue needs help) 192 Updated Oct 26, 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 7 Updated Oct 26, 2026
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream's past year of commit activity
    Nextflow 118 MIT 69 11 3 Updated Oct 26, 2026
  • proteinfamilies Public

    Generation and updating of protein families

    nf-core/proteinfamilies's past year of commit activity
    Nextflow 23 MIT 5 15 1 Updated Oct 26, 2026
  • proteinannotator Public

    Generation of sequence-level annotations for amino acid sequences

    nf-core/proteinannotator's past year of commit activity
    Nextflow 16 MIT 12 20 4 Updated Oct 26, 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 26, 2026
  • pathogenepidemiology Public

    [DEVELOPMENT UNDERWAY] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

    nf-core/pathogenepidemiology's past year of commit activity
    Nextflow 4 MIT 2 21 (2 issues need help) 3 Updated Oct 26, 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 11 Updated Oct 26, 2026
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