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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 257 203

  2. modules modules Public

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

    Nextflow 355 854

  3. rnaseq rnaseq Public

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

    Nextflow 1k 756

  4. sarek sarek Public

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

    Nextflow 442 443

  5. configs configs Public

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

    Nextflow 99 309

  6. proposals proposals Public

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

    8 1

Repositories

Showing 10 of 161 repositories
  • test-datasets Public

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

    nf-core/test-datasets’s past year of commit activity
    125 MIT 399 33 11 Updated May 14, 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 355 MIT 854 469 (1 issue needs help) 179 Updated May 14, 2025
  • proteinannotator Public

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

    nf-core/proteinannotator’s past year of commit activity
    Nextflow 4 MIT 5 23 8 Updated May 14, 2025
  • cellpainting Public
    nf-core/cellpainting’s past year of commit activity
    Nextflow 4 MIT 5 15 2 Updated May 14, 2025
  • pathogensurveillance Public

    Surveillance of pathogens using population genomics and sequencing

    nf-core/pathogensurveillance’s past year of commit activity
    Nextflow 23 MIT 7 59 (3 issues need help) 2 Updated May 14, 2025
  • bacass Public

    Simple bacterial assembly and annotation pipeline

    nf-core/bacass’s past year of commit activity
    Nextflow 74 MIT 60 32 (1 issue needs help) 7 Updated May 14, 2025
  • mhcquant Public

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    nf-core/mhcquant’s past year of commit activity
    Nextflow 35 MIT 29 11 (1 issue needs help) 2 Updated May 14, 2025
  • multiplesequencealign Public

    A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

    nf-core/multiplesequencealign’s past year of commit activity
    Nextflow 32 MIT 14 6 2 Updated May 14, 2025
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 78 MIT 48 66 (1 issue needs help) 4 Updated May 14, 2025
  • nf-utils Public

    Nextflow plugin for nf-core utils

    nf-core/nf-utils’s past year of commit activity
    Groovy 1 Apache-2.0 0 3 0 Updated May 14, 2025
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