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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 244 192

  2. modules modules Public

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

    Nextflow 287 731

  3. rnaseq rnaseq Public

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

    Nextflow 936 710

  4. sarek sarek Public

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

    Nextflow 411 417

  5. chipseq chipseq Public

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

    Nextflow 198 150

  6. eager eager Public

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

    Nextflow 151 82

Repositories

Showing 10 of 147 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 196 93 38 Updated Dec 11, 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 6 Updated Dec 10, 2024
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    nf-core/airrflow’s past year of commit activity
    Nextflow 54 MIT 35 20 3 Updated Dec 11, 2024
  • 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
    108 MIT 357 31 13 Updated Dec 10, 2024
  • fastqrepair Public

    A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered

    nf-core/fastqrepair’s past year of commit activity
    Nextflow 1 MIT 1 6 1 Updated Dec 10, 2024
  • rnaseq Public

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

    nf-core/rnaseq’s past year of commit activity
    Nextflow 936 MIT 710 66 14 Updated Dec 10, 2024
  • 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 66 MIT 37 64 (1 issue needs help) 5 Updated Dec 10, 2024
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 0 10 7 Updated Dec 10, 2024
  • fetchngs Public

    Pipeline to fetch metadata and raw FastQ files from public databases

    nf-core/fetchngs’s past year of commit activity
    Nextflow 153 MIT 73 23 7 Updated Dec 10, 2024
  • pixelator Public

    Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

    nf-core/pixelator’s past year of commit activity
    Nextflow 8 MIT 3 0 1 Updated Dec 10, 2024
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