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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 252 201

  2. modules modules Public

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

    Nextflow 349 829

  3. rnaseq 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 sarek Public

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

    Nextflow 435 437

  5. configs configs Public

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

    Nextflow 97 298

  6. proposals proposals Public

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

    3

Repositories

Showing 10 of 158 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 74 MIT 244 98 25 Updated Mar 29, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 40 10 Updated Mar 29, 2025
  • scdownstream Public

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

    nf-core/scdownstream’s past year of commit activity
    Nextflow 53 MIT 24 26 (3 issues need help) 4 Updated Mar 29, 2025
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq’s past year of commit activity
    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

    nf-core/createpanelrefs’s past year of commit activity
    Nextflow 8 MIT 8 7 2 Updated Mar 29, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 349 MIT 829 523 (1 issue needs help) 165 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

    nf-core/meerpipe’s past year of commit activity
    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

    nf-core/airrflow’s past year of commit activity
    Nextflow 58 MIT 40 23 3 Updated Mar 28, 2025
  • proteinfold Public

    Protein 3D structure prediction pipeline

    nf-core/proteinfold’s past year of commit activity
    Nextflow 77 MIT 55 38 (2 issues need help) 8 Updated Mar 28, 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
    120 MIT 388 33 10 Updated Mar 28, 2025
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