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@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

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  1. tools tools Public

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

    Python 245 192

  2. modules modules Public

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

    Nextflow 289 737

  3. rnaseq rnaseq Public

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

    Nextflow 956 716

  4. sarek sarek Public

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

    Nextflow 415 420

  5. chipseq chipseq Public

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

    Nextflow 204 149

  6. eager eager Public

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

    Nextflow 154 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 289 MIT 737 463 (1 issue needs help) 184 Updated Jan 13, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 70 MIT 194 90 37 Updated Jan 13, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 245 MIT 192 274 35 Updated Jan 13, 2025
  • spatialxe Public
    nf-core/spatialxe’s past year of commit activity
    Nextflow 7 MIT 3 30 3 Updated Jan 13, 2025
  • scnanoseq Public

    Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

    nf-core/scnanoseq’s past year of commit activity
    Nextflow 22 MIT 6 1 1 Updated Jan 13, 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 6 MIT 2 4 2 Updated Jan 13, 2025
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 14 MIT 8 18 (1 issue needs help) 2 Updated Jan 13, 2025
  • actions-runners Public

    Instructions and scripts for custom GitHub Actions runners

    nf-core/actions-runners’s past year of commit activity
    Shell 2 MIT 4 0 0 Updated Jan 13, 2025
  • sarek Public

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

    nf-core/sarek’s past year of commit activity
    Nextflow 415 MIT 420 266 (3 issues need help) 34 Updated Jan 13, 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
    109 MIT 362 31 15 Updated Jan 13, 2025