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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 290 743

  3. rnaseq rnaseq Public

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

    Nextflow 965 719

  4. sarek sarek Public

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

    Nextflow 417 421

  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 743 459 (1 issue needs help) 178 Updated Jan 25, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 226 MIT 115 58 (1 issue needs help) 11 Updated Jan 25, 2025
  • 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
    112 MIT 364 31 16 Updated Jan 25, 2025
  • dualrnaseq Public

    Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

    nf-core/dualrnaseq’s past year of commit activity
    Nextflow 20 MIT 33 15 8 Updated Jan 25, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 208 90 34 Updated Jan 25, 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 25, 2025
  • pacvar Public

    Longread PacBio sequencing processing for WGS and PureTarget

    nf-core/pacvar’s past year of commit activity
    Nextflow 3 MIT 2 1 2 Updated Jan 24, 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 965 MIT 719 64 13 Updated Jan 24, 2025
  • spatialxe Public
    nf-core/spatialxe’s past year of commit activity
    Nextflow 7 MIT 3 30 2 Updated Jan 24, 2025
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 14 MIT 9 19 (1 issue needs help) 2 Updated Jan 24, 2025
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