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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 232 187

  2. modules modules Public

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

    Nextflow 276 686

  3. rnaseq rnaseq Public

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

    Nextflow 869 695

  4. sarek sarek Public

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

    Nextflow 391 402

  5. chipseq chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 186 145

  6. eager eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Nextflow 142 80

Repositories

Showing 10 of 136 repositories
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 276 MIT 686 415 (1 issue needs help) 135 Updated Sep 20, 2024
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 23 8 Updated Sep 20, 2024
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    Astro 65 MIT 186 86 36 Updated Sep 20, 2024
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 232 MIT 187 253 50 Updated Sep 20, 2024
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 12 MIT 4 8 (1 issue needs help) 10 Updated Sep 20, 2024
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq’s past year of commit activity
    Nextflow 72 MIT 123 26 (1 issue needs help) 1 Updated Sep 19, 2024
  • 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
    101 MIT 338 31 9 Updated Sep 20, 2024
  • sarek Public

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

    nf-core/sarek’s past year of commit activity
    Nextflow 391 MIT 402 242 (2 issues need help) 33 Updated Sep 19, 2024
  • rnaseq Public

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

    nf-core/rnaseq’s past year of commit activity
    Nextflow 869 MIT 695 54 11 Updated Sep 19, 2024
  • atacseq Public

    ATAC-seq peak-calling and QC analysis pipeline

    nf-core/atacseq’s past year of commit activity
    Nextflow 179 MIT 116 25 3 Updated Sep 19, 2024
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