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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 245 192

  2. modules modules Public

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

    Nextflow 287 736

  3. rnaseq rnaseq Public

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

    Nextflow 941 713

  4. sarek sarek Public

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

    Nextflow 413 417

  5. chipseq chipseq Public

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

    Nextflow 200 150

  6. eager eager Public

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

    Nextflow 153 82

Repositories

Showing 10 of 148 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 70 MIT 195 93 40 Updated Dec 22, 2024
  • nascent Public

    Nascent Transcription Processing Pipeline

    nf-core/nascent’s past year of commit activity
    Nextflow 18 MIT 10 37 3 Updated Dec 22, 2024
  • fastqrepair Public

    A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered

    nf-core/fastqrepair’s past year of commit activity
    Nextflow 1 MIT 1 5 1 Updated Dec 22, 2024
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 287 MIT 736 464 (1 issue needs help) 187 Updated Dec 22, 2024
  • references Public
    nf-core/references’s past year of commit activity
    Nextflow 7 MIT 4 13 0 Updated Dec 22, 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
    109 MIT 361 31 15 Updated Dec 21, 2024
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 48 9 Updated Dec 21, 2024
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 0 9 10 Updated Dec 21, 2024
  • 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 66 MIT 39 77 (1 issue needs help) 6 Updated Dec 21, 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 941 MIT 713 63 12 Updated Dec 21, 2024
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