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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 Public

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

    Python 248 196

  2. modules Public

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

    Nextflow 294 754

  3. rnaseq Public

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

    Nextflow 990 728

  4. sarek Public

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

    Nextflow 426 430

Repositories

Showing 10 of 154 repositories
  • configs Public

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

    Nextflow 94 MIT 292 10 17 Updated Mar 10, 2025
  • website Public

    Code and files for the main nf-core website.

    MDX 72 MIT 228 92 30 Updated Mar 10, 2025
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    117 MIT 369 31 15 Updated Mar 10, 2025
  • modules Public

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

    Nextflow 294 MIT 754 640 (1 issue needs help) 149 Updated Mar 10, 2025
  • variantbenchmarking Public

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

    Nextflow 24 MIT 12 15 0 Updated Mar 10, 2025
  • genomeassembler Public

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

    Nextflow 19 MIT 13 5 0 Updated Mar 10, 2025
  • scrnaseq Public

    Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

    Nextflow 251 MIT 183 52 (1 issue needs help) 4 Updated Mar 10, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    Nextflow 42 MIT 37 15 1 Updated Mar 10, 2025
  • ops Public
    Python 1 2 33 9 Updated Mar 10, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    TypeScript 15 MIT 6 5 5 Updated Mar 10, 2025
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