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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 259 203

  2. modules modules Public

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

    Nextflow 355 863

  3. rnaseq rnaseq Public

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

    Nextflow 1k 765

  4. sarek sarek Public

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

    Nextflow 449 446

  5. configs configs Public

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

    Nextflow 99 311

  6. proposals proposals Public

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

    8 2

Repositories

Showing 10 of 163 repositories
  • variantbenchmarking Public

    Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 29 MIT 15 24 1 Updated Jun 6, 2025
  • 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 1,037 MIT 765 59 9 Updated Jun 6, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 238 MIT 132 61 (1 issue needs help) 10 Updated Jun 6, 2025
  • tfactivity Public

    Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

    nf-core/tfactivity’s past year of commit activity
    Nextflow 12 MIT 5 2 3 Updated Jun 6, 2025
  • genomeassembler Public

    Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads

    nf-core/genomeassembler’s past year of commit activity
    Nextflow 25 MIT 16 3 2 Updated Jun 6, 2025
  • 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 20 MIT 4 7 4 Updated Jun 6, 2025
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq’s past year of commit activity
    Nextflow 206 MIT 138 21 4 Updated Jun 6, 2025
  • eager Public

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

    nf-core/eager’s past year of commit activity
    Nextflow 169 MIT 83 45 (2 issues need help) 6 Updated Jun 6, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 259 MIT 203 267 39 Updated Jun 6, 2025
  • createtaxdb Public

    Parallelised and automated construction of metagenomic classifier databases of different tools

    nf-core/createtaxdb’s past year of commit activity
    Nextflow 9 MIT 7 7 1 Updated Jun 6, 2025
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