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    • nf-test

      Public
      A collection of test pipelines for nextflow to test with Flow
      Shell
      MIT License
      0000Updated Apr 24, 2026Apr 24, 2026
    • Python wrapper around Nextflow.
      Python
      GNU General Public License v3.0
      76210Updated Mar 20, 2026Mar 20, 2026
    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      MIT License
      105000Updated Mar 13, 2026Mar 13, 2026
    • flowbio

      Public
      A python library for interacting with the Flow API
      Python
      MIT License
      0000Updated Mar 13, 2026Mar 13, 2026
    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      MIT License
      864000Updated Jan 28, 2026Jan 28, 2026
    • A Nextflow DSL2 pipeline to perform ribo-seq data analysis and comprehensive quality control.
      R
      GNU General Public License v3.0
      5000Updated Nov 25, 2025Nov 25, 2025
    • hic

      Public
      Analysis of Chromosome Conformation Capture data (Hi-C)
      Nextflow
      MIT License
      67000Updated Oct 27, 2025Oct 27, 2025
    • clipseq

      Public
      The primary analysis pipeline for CLIP samples.
      Nextflow
      MIT License
      7221Updated Oct 16, 2025Oct 16, 2025
    • chipseq

      Public
      ChIP-seq peak-calling, QC and differential analysis pipeline.
      Nextflow
      MIT License
      175001Updated Oct 6, 2025Oct 6, 2025
    • Some examples of how to interact with the Flow API
      Jupyter Notebook
      0000Updated Oct 5, 2025Oct 5, 2025
    • A single cell transcriptomics pipeline for QC, integration and making the data presentable
      Nextflow
      MIT License
      61000Updated 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
      52000Updated Jul 13, 2025Jul 13, 2025
    • wf-aav-qc

      Public
      Python
      Other
      10000Updated Jul 12, 2025Jul 12, 2025
    • ampliseq

      Public
      Amplicon sequencing analysis workflow using DADA2 and QIIME2
      Nextflow
      MIT License
      151000Updated Jul 11, 2025Jul 11, 2025
    • rnavar

      Public
      gatk4 RNA variant calling pipeline
      Nextflow
      MIT License
      46000Updated 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
      528000Updated Jul 7, 2025Jul 7, 2025
    • Nextflow
      MIT License
      1000Updated Jun 21, 2025Jun 21, 2025
    • flow-nf

      Public
      Reusable modules used in Flow
      Nextflow
      MIT License
      0002Updated Dec 1, 2024Dec 1, 2024
    • Contains wrapper pipelines around nf-core modules
      Nextflow
      0000Updated Dec 1, 2024Dec 1, 2024
    • scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      MIT License
      214000Updated Dec 1, 2024Dec 1, 2024
    • R
      0001Updated Oct 6, 2024Oct 6, 2024
    • scflow

      Public
      Complete analysis workflow for single-cell/nuclei RNA-sequencing data.
      Nextflow
      MIT License
      14000Updated Nov 17, 2023Nov 17, 2023
    • fetchngs

      Public
      Pipeline to fetch metadata and raw FastQ files from public and private databases
      Nextflow
      MIT License
      90000Updated Nov 13, 2023Nov 13, 2023
    • tools

      Public
      Python package with helper tools for the nf-core community.
      Python
      MIT License
      239000Updated 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
      70000Updated Mar 30, 2023Mar 30, 2023
    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      MIT License
      132000Updated Dec 8, 2022Dec 8, 2022
    • Testing building mulled containers for multi-requirement tools.
      236000Updated Oct 29, 2022Oct 29, 2022
    • The Demultiplex pipeline used in Flow, using Ultraplex.
      0000Updated Oct 8, 2022Oct 8, 2022
    • imaps-nf

      Public
      Nextflow
      2041Updated Sep 26, 2022Sep 26, 2022
    • ultraplex

      Public
      Ultra-fast 5' and 3' demultiplexer
      Python
      Other
      12000Updated Aug 30, 2021Aug 30, 2021
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