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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 252 201

  2. modules Public

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

    Nextflow 349 829

  3. rnaseq Public

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

    Nextflow 1k 746

  4. sarek Public

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

    Nextflow 436 437

  5. configs Public

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

    Nextflow 97 298

  6. proposals Public

    Where new ideas for nf-core pipelines and more are proposed

    3

Repositories

Showing 10 of 158 repositories
  • proteinannotator Public

    The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations

    Nextflow 1 MIT 3 9 4 Updated Mar 30, 2025
  • modules Public

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

    Nextflow 349 MIT 829 523 (1 issue needs help) 168 Updated Mar 30, 2025
  • ops Public
    Python 1 2 40 10 Updated Mar 30, 2025
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    Nextflow 97 MIT 44 37 4 Updated Mar 30, 2025
  • website Public

    Code and files for the main nf-core website.

    MDX 74 MIT 244 98 26 Updated Mar 30, 2025
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    Nextflow 53 MIT 24 26 (3 issues need help) 4 Updated Mar 29, 2025
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    Nextflow 194 MIT 130 19 4 Updated Mar 29, 2025
  • createpanelrefs Public

    Generate Panel of Normals, models or other similar references from lots of samples

    Nextflow 8 MIT 8 7 2 Updated Mar 29, 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

    Nextflow 7 MIT 5 2 1 Updated Mar 29, 2025
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    Nextflow 58 MIT 40 23 3 Updated Mar 28, 2025
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