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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 260 204

  2. modules modules Public

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

    Nextflow 358 877

  3. rnaseq rnaseq Public

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

    Nextflow 1.1k 772

  4. sarek sarek Public

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

    Nextflow 453 450

  5. configs configs Public

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

    Nextflow 100 314

  6. proposals proposals Public

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

    8 3

Repositories

Showing 10 of 164 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 358 MIT 877 427 (1 issue needs help) 180 Updated Jul 1, 2025
  • ops Public

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

    nf-core/ops’s past year of commit activity
    Python 2 2 33 10 Updated Jul 1, 2025
  • 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 453 MIT 450 295 (6 issues need help) 40 Updated Jul 1, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 245 88 13 Updated Jul 1, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 1 2 16 4 Updated Jul 1, 2025
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    Nextflow 82 MIT 58 42 (2 issues need help) 6 Updated Jul 1, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 33 MIT 7 58 (3 issues need help) 1 Updated Jul 1, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 260 MIT 204 272 31 Updated Jul 1, 2025
  • genomeassembler Public

    Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads

    nf-core/genomeassembler’s past year of commit activity
    Nextflow 26 MIT 17 3 1 Updated Jul 1, 2025
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval’s past year of commit activity
    Nextflow 20 MIT 4 7 2 Updated Jul 1, 2025
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