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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 257 203

  2. modules modules Public

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

    Nextflow 355 857

  3. rnaseq rnaseq Public

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

    Nextflow 1k 756

  4. sarek sarek Public

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

    Nextflow 442 444

  5. configs configs Public

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

    Nextflow 99 309

  6. proposals proposals Public

    Where new ideas for nf-core pipelines, special interest groups and more are proposed

    8 1

Repositories

Showing 10 of 161 repositories
  • fetchngs Public

    Pipeline to fetch metadata and raw FastQ files from public databases

    nf-core/fetchngs’s past year of commit activity
    Nextflow 175 MIT 81 32 11 Updated May 16, 2025
  • nf-utils Public

    Nextflow plugin for nf-core utils

    nf-core/nf-utils’s past year of commit activity
    Groovy 1 Apache-2.0 0 3 0 Updated May 16, 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 355 MIT 857 462 (1 issue needs help) 187 Updated May 16, 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 1 Updated May 16, 2025
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 76 MIT 246 94 32 Updated May 16, 2025
  • spatialxe Public
    nf-core/spatialxe’s past year of commit activity
    Nextflow 19 MIT 9 26 3 Updated May 16, 2025
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 78 MIT 48 66 (1 issue needs help) 4 Updated May 16, 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
    126 MIT 400 33 12 Updated May 16, 2025
  • mag Public

    Assembly and binning of metagenomes

    nf-core/mag’s past year of commit activity
    Nextflow 237 MIT 126 62 (1 issue needs help) 11 Updated May 16, 2025
  • circrna Public

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

    nf-core/circrna’s past year of commit activity
    Nextflow 54 MIT 30 17 3 Updated May 16, 2025
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