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@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

nf-core logo nf-core logo

Welcome to @nf-core!

@nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow (@nextflow-io).

Here's how to get started:

Pinned

  1. tools Public

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

    Python 147 99

  2. modules Public

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

    Nextflow 103 217

  3. rnaseq Public

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

    Nextflow 452 432

  4. chipseq Public

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

    Nextflow 110 91

  5. sarek Public

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

    Nextflow 166 233

  6. eager Public

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

    Nextflow 64 56

Repositories

  • nascent Public

    Nascent Transcription Processing Pipeline

    Nextflow 3 MIT 7 9 1 Updated May 3, 2022
  • tools Public

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

    Python 147 MIT 99 76 10 Updated May 3, 2022
  • modules Public

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

    Nextflow 103 MIT 217 171 (6 issues need help) 51 Updated May 3, 2022
  • sarek Public

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

    Nextflow 166 MIT 233 64 (4 issues need help) 4 Updated May 3, 2022
  • hicar Public

    This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

    Nextflow 2 MIT 2 0 0 Updated May 3, 2022
  • nf-co.re Public

    Code and files for the main nf-core website.

    PHP 35 MIT 83 68 9 Updated May 3, 2022
  • rnafusion Public

    RNA-seq analysis pipeline for detection gene-fusions

    Nextflow 70 MIT 49 2 2 Updated May 3, 2022
  • test-datasets Public

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

    48 MIT 160 3 11 Updated May 3, 2022
  • configs Public

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

    Nextflow 44 MIT 134 13 (1 issue needs help) 7 Updated May 3, 2022
  • circdna Public

    Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

    Python 3 MIT 1 0 1 Updated May 3, 2022
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