Repositories list

• nf_splicing

  Public
  A nextflow pipeline of identifying and quantifying splicing events

  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 10, 2025Oct 10, 2025

• backup-plans

  Public
  Go

  •0•0•0•2•Updated Oct 10, 2025Oct 10, 2025

• wrstat-ui

  Public
  Go

  •

  MIT License

  •0•0•0•2•Updated Oct 10, 2025Oct 10, 2025

• spack-repo

  Public
  Spack Package Repository

  Python

  •

  MIT License

  •5•2•0•0•Updated Oct 10, 2025Oct 10, 2025

• wxs-qc

  Public
  Quality control pipeline for human exome/genome cohorts

  Python

  •

  Other

  •0•3•0•0•Updated Oct 9, 2025Oct 9, 2025

• yascp

  Public
  scRNA multimodal analysis pipeline utilised for large dataset processing - capable in handeling scRNA, scATAC, Hastag Multiplexed samples

  scrna-seq-analysis

  Python

  •

  GNU General Public License v3.0

  •7•15•0•0•Updated Oct 5, 2025Oct 5, 2025

• osdataproc

  Public
  osdataproc is a command-line tool for creating an OpenStack cluster with Apache Spark and Apache Hadoop configured. It comes with JupyterLab and Hail, a genomic data analysis library built on Spark installed, as well as Netdata for monitoring.

  Jinja

  •

  Other

  •3•0•0•0•Updated Oct 5, 2025Oct 5, 2025

• SSDV

  Public
  JavaScript

  •3•2•0•0•Updated Oct 1, 2025Oct 1, 2025

• softpack-builder

  Public
  SoftPack Builder provides services for building SoftPack environments

  Python

  •

  MIT License

  •0•0•1•16•Updated Oct 1, 2025Oct 1, 2025

• mercuryrc

  Public
  Shell

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 29, 2025Sep 29, 2025

• QTLight

  Public
  eqtl analysis pipeline using tensorqtl, saige-qtl, LIMIX, quasar and jaxQTL

  Python

  •

  GNU General Public License v3.0

  •8•13•0•0•Updated Sep 28, 2025Sep 28, 2025

• softpack-docs

  Public
  SoftPack Documentation

  JavaScript

  •0•0•5•20•Updated Sep 26, 2025Sep 26, 2025

• sarek

  Public
  Nextflow

  •

  MIT License

  •3•0•0•1•Updated Sep 24, 2025Sep 24, 2025

• backup-plan-ui

  Public
  A web-based user interface for managing backup plans. This application allows users to view, add, edit, and delete backup plan entries stored in a CSV file, SQLite or MySQL database..

  Go

  •

  MIT License

  •0•0•0•2•Updated Sep 22, 2025Sep 22, 2025

• nf_vep_annotation

  Public
  Run VEP and extract variant annotations

  Nextflow

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 22, 2025Sep 22, 2025

• nf_tower_irods_to_lustre

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •1•1•1•0•Updated Sep 19, 2025Sep 19, 2025

• wtsi-hgi.github.io

  Public
  Github webpage for HGI projects

  HTML

  •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

• ibackup-devkit

  Public
  Go

  •

  MIT License

  •0•0•0•1•Updated Sep 15, 2025Sep 15, 2025

• ibackup

  Public
  Performant backups of many files to iRODS

  Go

  •

  MIT License

  •0•0•0•3•Updated Sep 11, 2025Sep 11, 2025

• nf_splicing_qc

  Public
  a pipeline of sequencing data QC for splicing analysis

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 9, 2025Sep 9, 2025

• farmers-report

  Public
  Weekly report for farm usage

  R

  •0•0•0•1•Updated Sep 5, 2025Sep 5, 2025

• movie-server

  Public
  Go

  •1•0•0•0•Updated Sep 5, 2025Sep 5, 2025

• r-spack-recipe-builder

  Public
  Spack recipe creator for R packages in CRAN and Bioconductor used to build up the ubeR module for use in farm22

  Python

  •0•0•0•1•Updated Sep 2, 2025Sep 2, 2025

• softpack-mcp

  Public
  FastAPI-based MCP server for connecting softpack spack building commands to external services and LLMs

  Python

  •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

• softpack-vm-setup

  Public
  Shell scripts and ansible playbooks for setup of an Openstack VM for Softpack admin (build / test)

  Shell

  •0•0•0•0•Updated Aug 22, 2025Aug 22, 2025

• hgi-cloud

  Public
  terraform and ansible codebase to provision clusters (e.g. hail/spark) at Sanger

  ansiblesparkpacker+ 4terraformopenstackiachail

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•1•2•1•Updated Aug 21, 2025Aug 21, 2025

• tickets-search

  Public
  Search through legacy RT and Jira tickets

  Python

  •0•0•0•0•Updated Aug 9, 2025Aug 9, 2025

• rna_seq

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •2•0•1•0•Updated Jul 28, 2025Jul 28, 2025

• dmscore

  Public
  Nextflow

  •

  MIT License

  •2•0•0•0•Updated Jul 22, 2025Jul 22, 2025

• autoconvey

  Public
  Go

  •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025