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    129 repositories

    • 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•8•7•4•Updated Nov 17, 2024Nov 17, 2024

    • orcabus

      Public
       🐋 UMCCR Pipeline & Workflow Orchestration
      Python
      •0•4•47•6•Updated Nov 17, 2024Nov 17, 2024

    • data-portal-client

      Public
      UMCCR Data Portal Frontend
      TypeScript
      •1•1•6•1•Updated Nov 15, 2024Nov 15, 2024

    • cargo-lambda-cdk

      Public
      CDK Construct to build Rust functions with Cargo Lambda
      Go
      •
      MIT License
      •9•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      awsterraforminfrastructure
      Python
      •8•10•13•2•Updated Nov 15, 2024Nov 15, 2024

    • steps-s3-copy

      Public
      A Steps orchestration for copying large volumes of S3 objects
      TypeScript
      •
      MIT License
      •0•0•2•0•Updated Nov 15, 2024Nov 15, 2024

    • gpgr

      Public
      📚 Genomics Platform Group Reporter
      rcancer-genomics
      R
      •
      Other
      •1•8•0•1•Updated Nov 14, 2024Nov 14, 2024

    • orca-ui

      Public
      TypeScript
      •
      MIT License
      •0•0•16•1•Updated Nov 14, 2024Nov 14, 2024

    • rportal

      Public
      🔮 R functionality for UMCCR Data Portal
      R
      •
      Other
      •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • data-portal-apis

      Public
      UMCCR Data Portal API Backend in cloud native serverless
      Python
      •0•1•19•0•Updated Nov 14, 2024Nov 14, 2024

    • libumccr

      Public
      🐍 UMCCR Reusable Python modules
      Python
      •
      MIT License
      •0•0•4•0•Updated Nov 14, 2024Nov 14, 2024

    • nextflow-stack

      Public
      AWS stack to run Nextflow pipelines on Batch using shared resources
      Shell
      •0•0•2•1•Updated Nov 14, 2024Nov 14, 2024

    • dracarys

      Public
      🐲 DRAGEN workflow tidying 🔥
      cancer-genomicsmultiqcr-packager6qcdragen
      R
      •
      Other
      •0•0•24•1•Updated Nov 12, 2024Nov 12, 2024

    • cwl-novice-tutorial

      Public
      CWL Novice Tutorial
      cwl
      HTML
      •
      Other
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • v2-samplesheet-maker

      Public
      Generate V2 SampleSheets from JSON Inputs
      Python
      •
      MIT License
      •0•4•0•0•Updated Nov 11, 2024Nov 11, 2024

    • RNAsum

      Public
      Pipeline for generating RNAseq-based cancer patient reports
      rnaseq-pipelinernaseq-report
      R
      •
      Other
      •4•7•16•0•Updated Nov 8, 2024Nov 8, 2024

    • illumination

      Public
      🔆 Interacting with Illumina Connected Analytics (ICA) API
      expressejsnodejs
      EJS
      •2•3•1•1•Updated Nov 8, 2024Nov 8, 2024

    • cwl-ica-cli

      Public
      The CLI used for creating/syncing CWL workflows from GitHub to ICAv1
      Python
      •
      MIT License
      •0•1•13•0•Updated Nov 6, 2024Nov 6, 2024

    • htsget-rs

      Public
      A server implementation of the htsget protocol for bioinformatics in Rust
      rustbioinformaticsaws-lambdaserverlesshtsgetbioinfonoodles
      Rust
      •
      MIT License
      •9•39•19•5•Updated Nov 6, 2024Nov 6, 2024

    • linxreport

      Public
      Linx Result Reporter
      R
      •
      Other
      •0•1•0•0•Updated Nov 4, 2024Nov 4, 2024

    • samplesheet-check-frontend

      Public
      JavaScript
      •0•0•2•1•Updated Oct 28, 2024Oct 28, 2024

    • pcgr

      Public
      Personal Cancer Genome Reporter (PCGR)
      R
      •
      MIT License
      •48•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • holmes

      Public
      BAM fingerprint stack
      TypeScript
      •
      MIT License
      •0•3•4•1•Updated Oct 9, 2024Oct 9, 2024

    • crypt4gh-rust

      Public
      Rust implementation for the Crypt4GH encryption format
      Rust
      •
      Apache License 2.0
      •2•0•0•1•Updated Oct 8, 2024Oct 8, 2024

    • variant-tally

      Public
      Computes tallies of occurrence of variation across laboratories
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • sk-explore

      Public
      HTML
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • data-portal-status-page

      Public archive
      TypeScript
      •0•0•5•0•Updated Sep 24, 2024Sep 24, 2024

    • samplesheet-check-backend

      Public
      Python
      •0•0•2•0•Updated Sep 16, 2024Sep 16, 2024

    • docker-who

      Public
      A miscellaneous set of UMCCR dockerfiles that don't quite go anywhere else.
      Dockerfile
      •
      MIT License
      •0•3•1•0•Updated Sep 2, 2024Sep 2, 2024

    • wrapica

      Public
      A suite of secondary / tertiary functions for running ICA API calls
      Python
      •
      GNU General Public License v3.0
      •0•2•10•1•Updated Aug 30, 2024Aug 30, 2024