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    113 repositories

    • orcabus

      Public
       🐋 UMCCR Pipeline & Workflow Orchestration
      Python
      •0•5•35•12•Updated Jun 20, 2025Jun 20, 2025

    • rportal

      Public
      🔮 R functionality for UMCCR Data Portal
      R
      •
      Other
      •0•0•1•0•Updated Jun 20, 2025Jun 20, 2025

    • nextflow-stack

      Public
      AWS stack to run Nextflow pipelines on Batch using shared resources
      Shell
      •1•0•3•3•Updated Jun 20, 2025Jun 20, 2025

    • sash

      Public
      Nextflow
      •
      MIT License
      •0•0•1•1•Updated Jun 19, 2025Jun 19, 2025

    • bolt

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•2•1•Updated Jun 19, 2025Jun 19, 2025

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      HCL
      •0•0•9•0•Updated Jun 18, 2025Jun 18, 2025

    • cwl-ica

      Public
      A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide
      Common Workflow Language
      •
      MIT License
      •2•10•7•5•Updated Jun 17, 2025Jun 17, 2025

    • cwl-ica-cli

      Public
      The CLI used for creating/syncing CWL workflows from GitHub to ICAv1
      Python
      •
      MIT License
      •0•1•13•0•Updated Jun 17, 2025Jun 17, 2025

    • steps-s3-copy

      Public
      A Steps orchestration for copying large volumes of S3 objects
      TypeScript
      •
      MIT License
      •0•0•10•1•Updated Jun 13, 2025Jun 13, 2025

    • orca-ui

      Public
      TypeScript
      •
      MIT License
      •0•1•18•0•Updated Jun 12, 2025Jun 12, 2025

    • libica

      Public
      🐍 Python SDK for Illumina Connected Analytics (ICA) 🐉
      Python
      •
      MIT License
      •4•6•0•0•Updated Jun 6, 2025Jun 6, 2025

    • tgv

      Public
      Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.
      Rust
      •
      MIT License
      •13•2•0•0•Updated Jun 6, 2025Jun 6, 2025

    • ega-submit

      Public
      EGA cryptor + Aspera CLI submitter
      Shell
      •0•0•0•0•Updated Jun 5, 2025Jun 5, 2025

    • gpgr

      Public
      📚 Genomics Platform Group Reporter
      rcancer-genomics
      R
      •
      Other
      •1•8•2•0•Updated Jun 5, 2025Jun 5, 2025

    • htsget-deploy

      Public
      Deployment logic for htsget-rs
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • bwa-mem2-perf

      Public
      CI benchmarking for bwa-mem2
      0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • copyrite

      Public
      A CLI tool for efficient checksum/copy operations across object stores
      awsclouds3gcs
      Rust
      •
      MIT License
      •0•2•16•1•Updated May 28, 2025May 28, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.5k•0•0•0•Updated May 27, 2025May 27, 2025

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      awsterraforminfrastructure
      Python
      •8•10•10•3•Updated May 26, 2025May 26, 2025

    • crypt4gh-rust

      Public
      Rust implementation for the Crypt4GH encryption format
      Rust
      •2•0•0•1•Updated May 26, 2025May 26, 2025

    • RNAsum

      Public
      Pipeline for generating RNAseq-based cancer patient reports
      rnaseq-pipelinernaseq-report
      R
      •
      Other
      •4•7•16•0•Updated May 26, 2025May 26, 2025

    • orcahouse-doc

      Public
      📘 Warehouse Documentation
      HTML
      •0•0•0•0•Updated May 23, 2025May 23, 2025

    • WTS_workflow_results_comparison

      Public
      R
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • hmftools

      Public
      UMCCR custom fork of hmftools, mainly for Aarch64 migration testing purposes
      Java
      •
      GNU General Public License v3.0
      •60•0•0•0•Updated May 15, 2025May 15, 2025

    • gatk-bwamem-jni

      Public
      JNI code for bwa mem
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 15, 2025May 15, 2025

    • bwa

      Public
      Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
      C
      •
      Apache License 2.0
      •563•0•0•0•Updated May 15, 2025May 15, 2025

    • sk-explore

      Public
      HTML
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • data-portal-client

      Public archive
      Superseded By OrcaUI/OrcaBus - UMCCR Data Portal Frontend
      TypeScript
      •1•1•0•0•Updated May 6, 2025May 6, 2025

    • project-sightseeing

      Public
      0•0•3•0•Updated May 6, 2025May 6, 2025

    • htsget-rs

      Public
      A server implementation of the htsget protocol for bioinformatics in Rust
      rustbioinformaticsaws-lambdaserverlesshtsgetbioinfonoodles
      Rust
      •
      MIT License
      •10•45•14•3•Updated Apr 28, 2025Apr 28, 2025