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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 256 201

  2. modules modules Public

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

    Nextflow 355 838

  3. rnaseq rnaseq Public

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

    Nextflow 1k 752

  4. sarek sarek Public

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

    Nextflow 441 443

  5. configs configs Public

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

    Nextflow 98 306

  6. proposals proposals Public

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

    8

Repositories

Showing 10 of 160 repositories
  • methylong Public

    Extract methylation calls from long reads (ONT/ PacBio)

    nf-core/methylong’s past year of commit activity
    6 MIT 1 1 2 Updated Apr 27, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 75 MIT 245 95 25 Updated Apr 27, 2025
  • fetchngs Public

    Pipeline to fetch metadata and raw FastQ files from public databases

    nf-core/fetchngs’s past year of commit activity
    Nextflow 174 MIT 80 29 11 Updated Apr 27, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 1 2 13 2 Updated Apr 26, 2025
  • tfactivity Public

    Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

    nf-core/tfactivity’s past year of commit activity
    Nextflow 12 MIT 4 1 0 Updated Apr 26, 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 54 MIT 23 25 (3 issues need help) 1 Updated Apr 26, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 2 2 30 10 Updated Apr 26, 2025
  • reportho Public

    nf-core pipeline for comparative analysis of ortholog predictions

    nf-core/reportho’s past year of commit activity
    Nextflow 11 MIT 6 6 1 Updated Apr 26, 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 60 MIT 41 22 5 Updated Apr 25, 2025
  • logos Public

    Host nf-core logos and templates for making new logos

    nf-core/logos’s past year of commit activity
    6 MIT 13 0 0 Updated Apr 25, 2025
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