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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 233 187

  2. modules modules Public

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

    Nextflow 276 691

  3. rnaseq rnaseq Public

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

    Nextflow 874 697

  4. sarek sarek Public

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

    Nextflow 393 403

  5. chipseq chipseq Public

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

    Nextflow 187 145

  6. eager eager Public

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

    Nextflow 143 80

Repositories

Showing 10 of 136 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    Astro 66 MIT 187 87 38 Updated Oct 1, 2024
  • nft-utils Public

    nf-test utility functions

    nf-core/nft-utils’s past year of commit activity
    Java 5 MIT 3 1 1 Updated Oct 1, 2024
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 233 MIT 187 246 39 Updated Oct 1, 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 57 MIT 32 38 4 Updated Oct 1, 2024
  • configs Public

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

    nf-core/configs’s past year of commit activity
    Nextflow 85 MIT 264 9 13 Updated Oct 1, 2024
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 126 MIT 35 39 (1 issue needs help) 4 Updated Oct 1, 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 393 MIT 403 243 (2 issues need help) 33 Updated Oct 1, 2024
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 23 10 Updated Oct 1, 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 276 MIT 691 425 (1 issue needs help) 136 Updated Oct 1, 2024
  • multiplesequencealign Public

    A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

    nf-core/multiplesequencealign’s past year of commit activity
    Nextflow 13 MIT 11 1 2 Updated Oct 1, 2024
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