Skip to content

@umccr UMCCR

Change the repository type filter

All

    Repositories list

    110 repositories

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      HCL
      •0•0•5•0•Updated Apr 12, 2025Apr 12, 2025

    • orca-ui

      Public
      TypeScript
      •
      MIT License
      •0•1•18•1•Updated Apr 11, 2025Apr 11, 2025

    • orcabus

      Public
       🐋 UMCCR Pipeline & Workflow Orchestration
      Python
      •0•5•85•19•Updated Apr 11, 2025Apr 11, 2025

    • bolt

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•2•1•Updated Apr 11, 2025Apr 11, 2025

    • nagim-clinical-data-sharing

      Public
      Pilot of software for NAGIM clinical data sharing
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • nextflow-stack

      Public
      AWS stack to run Nextflow pipelines on Batch using shared resources
      Shell
      •1•0•2•3•Updated Apr 10, 2025Apr 10, 2025

    • orcahouse-doc

      Public
      📘 Warehouse Documentation
      HTML
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • cloud-checksum

      Public
      A CLI tool for checksum/copy operations across multiple cloud object stores
      Rust
      •
      MIT License
      •0•0•18•2•Updated Apr 9, 2025Apr 9, 2025

    • sash

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • v2-samplesheet-parser

      Public
      A lightweight tool to parse and validate V2 SampleSheets from multiple formats.
      MIT License
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • dracarys

      Public
      🐲 DRAGEN workflow tidying 🔥
      cancer-genomicsmultiqcr-packager6qcdragen
      R
      •
      Other
      •0•0•30•0•Updated Apr 7, 2025Apr 7, 2025

    • oncoanalyser-aws

      Public
      TypeScript
      •1•0•6•1•Updated Apr 7, 2025Apr 7, 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 Apr 7, 2025Apr 7, 2025

    • RNAsum

      Public
      Pipeline for generating RNAseq-based cancer patient reports
      rnaseq-pipelinernaseq-report
      R
      •
      Other
      •4•7•16•1•Updated Apr 7, 2025Apr 7, 2025

    • steps-s3-copy

      Public
      A Steps orchestration for copying large volumes of S3 objects
      TypeScript
      •
      MIT License
      •0•0•7•1•Updated Apr 1, 2025Apr 1, 2025

    • rems-umccr

      Public
      A Docker image of REMS built for deployment in AWS and setup for UMCCR configuration
      TypeScript
      •
      MIT License
      •0•0•0•1•Updated Apr 1, 2025Apr 1, 2025

    • sk-explore

      Public
      HTML
      •0•0•0•0•Updated Mar 31, 2025Mar 31, 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•9•7•6•Updated Mar 31, 2025Mar 31, 2025

    • samplesheet-check-backend

      Public archive
      Python
      •0•0•0•1•Updated Mar 30, 2025Mar 30, 2025

    • linxreport

      Public
      Linx Result Reporter
      R
      •
      Other
      •0•1•0•0•Updated Mar 24, 2025Mar 24, 2025

    • htsget-rs

      Public
      A server implementation of the htsget protocol for bioinformatics in Rust
      rustbioinformaticsaws-lambdaserverlesshtsgetbioinfonoodles
      Rust
      •
      MIT License
      •9•41•14•4•Updated Mar 24, 2025Mar 24, 2025

    • crypt4gh-rust

      Public
      Rust implementation for the Crypt4GH encryption format
      Rust
      •2•0•0•1•Updated Mar 24, 2025Mar 24, 2025

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      awsterraforminfrastructure
      Python
      •8•10•11•3•Updated Mar 21, 2025Mar 21, 2025

    • oncoanalyser-arm64

      Public
      ARM64 experiments for Oncoanalyser
      Nextflow
      •
      MIT License
      •17•0•0•0•Updated Mar 17, 2025Mar 17, 2025

    • reference-sequence-comparison

      Public
      Comparison of genomic alignment and variant calling performance using different reference sequences
      R
      •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • oncoanalyser-aws-example-setup

      Public
      An example of setting up Oncoanalyser in AWS
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • agha-data-validation-pipeline

      Public
      Python
      •0•0•2•0•Updated Mar 10, 2025Mar 10, 2025

    • gatk-bwamem-jni

      Public
      JNI code for bwa mem
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 8, 2025Mar 8, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.4k•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • pcgr

      Public
      Personal Cancer Genome Reporter (PCGR)
      R
      •
      MIT License
      •49•0•0•0•Updated Mar 5, 2025Mar 5, 2025