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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 252 198

  2. modules Public

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

    Nextflow 297 760

  3. rnaseq Public

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

    Nextflow 998 740

  4. sarek Public

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

    Nextflow 432 434

Repositories

Showing 10 of 157 repositories
  • website Public

    Code and files for the main nf-core website.

    MDX 74 MIT 243 93 32 Updated Mar 22, 2025
  • stats Public
    HTML 0 2 13 10 Updated Mar 22, 2025
  • tools Public

    Python package with helper tools for the nf-core community.

    Python 252 MIT 198 256 31 Updated Mar 22, 2025
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    Nextflow 97 MIT 43 36 3 Updated Mar 21, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    TypeScript 15 MIT 6 5 5 Updated Mar 21, 2025
  • ops Public
    Python 1 2 40 9 Updated Mar 21, 2025
  • rnavar Public

    gatk4 RNA variant calling pipeline

    Nextflow 44 MIT 37 13 1 Updated Mar 21, 2025
  • modules Public

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

    Nextflow 297 MIT 760 487 (1 issue needs help) 129 Updated Mar 21, 2025
  • clipseq Public

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

    Nextflow 21 MIT 30 28 3 Updated Mar 21, 2025
  • rnaseq Public

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

    Nextflow 998 MIT 740 81 15 Updated Mar 21, 2025
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