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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 252 200

  2. modules Public

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

    Nextflow 346 823

  3. rnaseq Public

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

    Nextflow 1k 745

  4. sarek Public

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

    Nextflow 434 437

Repositories

Showing 10 of 158 repositories
  • modules Public

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

    Nextflow 346 MIT 823 541 (1 issue needs help) 171 Updated Mar 26, 2025
  • bactmap Public

    A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

    Nextflow 53 MIT 51 23 (1 issue needs help) 1 Updated Mar 26, 2025
  • nft-utils Public

    nf-test utility functions

    Java 10 MIT 9 6 2 Updated Mar 26, 2025
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    118 MIT 383 33 12 Updated Mar 26, 2025
  • proteinfamilies Public

    Generation and update of protein families

    Nextflow 11 MIT 2 10 2 Updated Mar 26, 2025
  • lncpipe Public Forked from likelet/LncPipe

    UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

    Nextflow 34 MIT 52 23 (2 issues need help) 2 Updated Mar 26, 2025
  • seqinspector Public

    QC pipeline to inspect your sequences

    Nextflow 9 MIT 31 37 (3 issues need help) 11 Updated Mar 26, 2025
  • pixelator Public

    Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

    Nextflow 8 MIT 5 0 2 Updated Mar 26, 2025
  • tfactivity Public

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

    Nextflow 10 MIT 4 1 1 Updated Mar 26, 2025
  • clipseq Public

    CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

    Nextflow 21 MIT 40 33 8 Updated Mar 26, 2025
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