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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 246 192

  2. modules modules Public

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

    Nextflow 290 741

  3. rnaseq rnaseq Public

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

    Nextflow 964 716

  4. sarek sarek Public

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

    Nextflow 416 421

  5. chipseq chipseq Public

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

    Nextflow 203 149

  6. eager eager Public

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

    Nextflow 155 82

Repositories

Showing 10 of 150 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 290 MIT 741 463 (1 issue needs help) 180 Updated Jan 21, 2025
  • meerpipe Public

    nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis

    nf-core/meerpipe’s past year of commit activity
    Nextflow 7 MIT 4 0 1 Updated Jan 21, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 43 8 Updated Jan 21, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 70 MIT 205 91 34 Updated Jan 21, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 14 MIT 6 9 5 Updated Jan 21, 2025
  • pairgenomealign Public

    Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

    nf-core/pairgenomealign’s past year of commit activity
    Nextflow 6 MIT 3 10 1 Updated Jan 21, 2025
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    nf-core/oncoanalyser’s past year of commit activity
    Nextflow 57 MIT 11 15 3 Updated Jan 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 69 MIT 41 74 (1 issue needs help) 7 Updated Jan 20, 2025
  • scrnaseq Public

    A single-cell RNAseq pipeline for 10X genomics data

    nf-core/scrnaseq’s past year of commit activity
    Nextflow 224 MIT 177 53 (1 issue needs help) 2 Updated Jan 21, 2025
  • 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 2 5 1 Updated Jan 20, 2025
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