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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 358 878

  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 773

  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 165 repositories
  • 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 3, 2025
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 100 MIT 314 8 12 Updated Jul 3, 2025
  • coproid Public

    Coprolite host Identification pipeline

    nf-core/coproid’s past year of commit activity
    Nextflow 12 MIT 5 0 2 Updated Jul 2, 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 2, 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) 41 Updated Jul 2, 2025
  • 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 878 428 (1 issue needs help) 180 Updated Jul 2, 2025
  • rarevariantburden Public

    Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.

    nf-core/rarevariantburden’s past year of commit activity
    Nextflow 0 MIT 1 0 0 Updated Jul 2, 2025
  • fastquorum Public

    Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

    nf-core/fastquorum’s past year of commit activity
    Nextflow 23 MIT 16 10 (1 issue needs help) 1 Updated Jul 2, 2025
  • drop Public

    Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

    nf-core/drop’s past year of commit activity
    Nextflow 5 MIT 2 3 3 Updated Jul 2, 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) 4 Updated Jul 2, 2025
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