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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 256 201

  2. modules Public

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

    Nextflow 355 837

  3. rnaseq Public

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

    Nextflow 1k 749

  4. sarek Public

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

    Nextflow 439 441

  5. configs Public

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

    Nextflow 98 304

  6. proposals Public

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

    7

Repositories

Showing 10 of 159 repositories
  • modules Public

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

    Nextflow 355 MIT 837 491 (1 issue needs help) 181 Updated Apr 23, 2025
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    Nextflow 46 MIT 43 22 2 Updated Apr 23, 2025
  • methylarray Public

    Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.

    Nextflow 4 MIT 3 12 1 Updated Apr 23, 2025
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    Nextflow 152 MIT 109 33 (4 issues need help) 4 Updated Apr 23, 2025
  • website Public

    Code and files for the main nf-core website.

    MDX 75 MIT 246 95 25 Updated Apr 23, 2025
  • nascent Public

    Nascent Transcription Processing Pipeline

    Nextflow 19 MIT 11 40 5 Updated Apr 23, 2025
  • dualrnaseq Public

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

    Nextflow 22 MIT 35 37 8 Updated Apr 23, 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 8 MIT 5 2 1 Updated Apr 23, 2025
  • proteinannotator Public

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

    Nextflow 3 MIT 3 14 5 Updated Apr 22, 2025
  • circrna Public

    circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

    Nextflow 54 MIT 30 14 2 Updated Apr 22, 2025
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