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    29 repositories

    • nextflow.py

      Public
      Python wrapper around Nextflow.
      nextflowpipelines
      Python
      •
      GNU General Public License v3.0
      •7•62•1•0•Updated Feb 1, 2026Feb 1, 2026

    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      •
      MIT License
      •847•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • flowbio

      Public
      A python library for interacting with the Flow API
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • riboseq-flow

      Public
      A Nextflow DSL2 pipeline to perform ribo-seq data analysis and comprehensive quality control.
      R
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • hic

      Public
      Analysis of Chromosome Conformation Capture data (Hi-C)
      Nextflow
      •
      MIT License
      •65•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • clipseq

      Public
      The primary analysis pipeline for CLIP samples.
      Nextflow
      •
      MIT License
      •7•2•2•1•Updated Oct 16, 2025Oct 16, 2025

    • chipseq

      Public
      ChIP-seq peak-calling, QC and differential analysis pipeline.
      Nextflow
      •
      MIT License
      •166•0•0•1•Updated Oct 6, 2025Oct 6, 2025

    • flow-api-example-scripts

      Public
      Some examples of how to interact with the Flow API
      Jupyter Notebook
      •0•0•0•0•Updated Oct 5, 2025Oct 5, 2025

    • scdownstream

      Public
      A single cell transcriptomics pipeline for QC, integration and making the data presentable
      Nextflow
      •
      MIT License
      •53•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • airrflow

      Public
      B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
      Nextflow
      •
      MIT License
      •46•0•0•0•Updated Jul 13, 2025Jul 13, 2025

    • wf-aav-qc

      Public
      Python
      •
      Other
      •11•0•0•0•Updated Jul 12, 2025Jul 12, 2025

    • ampliseq

      Public
      Amplicon sequencing analysis workflow using DADA2 and QIIME2
      Nextflow
      •
      MIT License
      •145•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • rnavar

      Public
      gatk4 RNA variant calling pipeline
      Nextflow
      •
      MIT License
      •44•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •522•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • nf-quantseq

      Public
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jun 21, 2025Jun 21, 2025

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •105•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • flow-nf

      Public
      Reusable modules used in Flow
      Nextflow
      •
      MIT License
      •0•0•0•2•Updated Dec 1, 2024Dec 1, 2024

    • nfcore-wrappers

      Public
      Contains wrapper pipelines around nf-core modules
      Nextflow
      •0•0•0•0•Updated Dec 1, 2024Dec 1, 2024

    • scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      •
      MIT License
      •211•0•0•0•Updated Dec 1, 2024Dec 1, 2024

    • differential-analysis

      Public
      R
      •0•0•0•1•Updated Oct 6, 2024Oct 6, 2024

    • scflow

      Public
      Complete analysis workflow for single-cell/nuclei RNA-sequencing data.
      Nextflow
      •
      MIT License
      •14•0•0•0•Updated Nov 17, 2023Nov 17, 2023

    • fetchngs

      Public
      Pipeline to fetch metadata and raw FastQ files from public and private databases
      Nextflow
      •
      MIT License
      •88•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • tools

      Public
      Python package with helper tools for the nf-core community.
      Python
      •
      MIT License
      •224•0•0•0•Updated Jul 17, 2023Jul 17, 2023

    • cutandrun

      Public
      Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
      Nextflow
      •
      MIT License
      •68•0•0•0•Updated Mar 30, 2023Mar 30, 2023

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •133•0•0•0•Updated Dec 8, 2022Dec 8, 2022

    • multi-package-containers

      Public
      Testing building mulled containers for multi-requirement tools.
      233•0•0•0•Updated Oct 29, 2022Oct 29, 2022

    • flow-demultiplex

      Public
      The Demultiplex pipeline used in Flow, using Ultraplex.
      0•0•0•0•Updated Oct 8, 2022Oct 8, 2022

    • imaps-nf

      Public
      Nextflow
      •2•0•4•1•Updated Sep 26, 2022Sep 26, 2022

    • ultraplex

      Public
      Ultra-fast 5' and 3' demultiplexer
      Python
      •
      Other
      •12•0•0•0•Updated Aug 30, 2021Aug 30, 2021