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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 247 194

  2. modules modules Public

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

    Nextflow 292 752

  3. rnaseq rnaseq Public

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

    Nextflow 984 721

  4. sarek sarek Public

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

    Nextflow 424 428

  5. chipseq chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 206 149

  6. eager eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Nextflow 159 81

Repositories

Showing 10 of 154 repositories
  • phyloplace Public

    nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

    nf-core/phyloplace’s past year of commit activity
    Nextflow 7 MIT 4 1 0 Updated Feb 20, 2025
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 14 MIT 9 15 2 Updated Feb 20, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    nf-core/rnavar’s past year of commit activity
    Nextflow 41 MIT 36 38 4 Updated Feb 20, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 220 90 40 Updated Feb 20, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 247 MIT 194 281 41 Updated Feb 20, 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 72 MIT 42 74 (1 issue needs help) 4 Updated Feb 20, 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 292 MIT 752 463 (1 issue needs help) 190 Updated Feb 20, 2025
  • testpipeline Public

    A small example pipeline used to test new nf-core infrastructure and common code.

    nf-core/testpipeline’s past year of commit activity
    Nextflow 4 MIT 40 0 7 Updated Feb 20, 2025
  • genomeassembler Public
    nf-core/genomeassembler’s past year of commit activity
    Nextflow 17 MIT 13 1 3 Updated Feb 20, 2025
  • phaseimpute Public

    A bioinformatics pipeline to phase and impute genetic data

    nf-core/phaseimpute’s past year of commit activity
    Nextflow 19 MIT 15 14 5 Updated Feb 20, 2025
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