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@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

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  1. tools tools Public

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

    Python 242 191

  2. modules modules Public

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

    Nextflow 283 719

  3. rnaseq rnaseq Public

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

    Nextflow 912 708

  4. sarek sarek Public

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

    Nextflow 408 415

  5. chipseq chipseq Public

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

    Nextflow 194 149

  6. eager eager Public

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

    Nextflow 148 81

Repositories

Showing 10 of 145 repositories
  • 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 88 MIT 273 11 15 Updated Nov 16, 2024
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 283 MIT 719 450 (1 issue needs help) 158 Updated Nov 16, 2024
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 196 89 35 Updated Nov 16, 2024
  • 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 408 MIT 415 261 (3 issues need help) 35 Updated Nov 15, 2024
  • nanostring Public

    An analysis pipeline for Nanostring nCounter expression data.

    nf-core/nanostring’s past year of commit activity
    Nextflow 13 MIT 8 13 2 Updated Nov 15, 2024
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 12 MIT 5 8 (1 issue needs help) 3 Updated Nov 15, 2024
  • fastquorum Public

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

    nf-core/fastquorum’s past year of commit activity
    Nextflow 20 MIT 10 14 (1 issue needs help) 2 Updated Nov 15, 2024
  • nf-core/setup-nf-test’s past year of commit activity
    JavaScript 2 MIT 2 0 0 Updated Nov 15, 2024
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 242 MIT 191 251 33 Updated Nov 15, 2024
  • 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 4 MIT 1 4 1 Updated Nov 15, 2024