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    11 repositories

    • General_LW_scripts

      Public
      The scripts that UPHL uses to download things from basespace and run respective workflows
      bioinformatics
      Python
      •
      GNU General Public License v3.0
      •2•2•0•8•Updated Feb 25, 2025Feb 25, 2025

    • Cecret

      Public
      Reference-based consensus creation
      nextflowampliconsars-cov-2monkeypoxbioinformatics
      Nextflow
      •
      MIT License
      •27•51•4•0•Updated Feb 25, 2025Feb 25, 2025

    • walkercreek

      Public
      A nextflow pipeline that accommodates different sequencing technologies (Illumina or Nanopore), sample types (clinical or wastewater), and viral targets (Influenza or RSV).
      HTML
      •
      MIT License
      •1•8•1•0•Updated Feb 24, 2025Feb 24, 2025

    • Dockerfiles

      Public
      A collection of Dockerfiles for the images that we use
      Dockerfile
      •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

    • mycosnp-nf

      Public
      CDCgov/mycosnp-nf
      Nextflow
      •
      Apache License 2.0
      •39•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • Grandeur

      Public
      UPHL's Reference Free Pipeline
      dockernextflowsingularityilluminaserotypingprokaryotesbioinformaticsgenomicsngs
      Nextflow
      •
      GNU General Public License v3.0
      •7•25•7•0•Updated Feb 4, 2025Feb 4, 2025

    • Donut_Falls

      Public
      Basic workflow for nanopore sequencing data
      nanoporenextflowdenovo-assemblypolishingbioinformatics
      Nextflow
      •
      MIT License
      •7•15•7•0•Updated Feb 4, 2025Feb 4, 2025

    • Wastewater-genomic-analysis

      Public
      Python
      •0•1•1•0•Updated Aug 12, 2024Aug 12, 2024

    • ICA_Modified_Nextflow_Scripts

      Public
      To be able to run Nextflow scripts that are published on Github on ICA they must be modified because ICA does not have Nextflow do a gitpull and an ICA user cannot pass config or param files.
      nextflowica
      Nextflow
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 6, 2023Sep 6, 2023

    • Nextstrain_Build

      Public
      A Nextflow Script that performs a Nextstrain 'Build' which creates a detailed phylogentic visualization that can be seen with the Nextstain Auspice tool.
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Aug 26, 2022Aug 26, 2022

    • UPHL

      Public archive
      The fun things we use and share at UPHL
      Shell
      •
      MIT License
      •1•5•0•0•Updated Mar 11, 2021Mar 11, 2021