Discover wtsi-hgi/cookie-monster Open Source project

Generates CWL files from the GATK documentation

gatk-cwl-generator

yascp

scRNA analysis pipeline

Etherpad Lite plugin to trust authentication passed in from X-Forwarded-User HTTP header. This is useful when running behind a reverse proxy (a "series of tubes") that handles authentication. Do not use this plugin unless you have protected the server so that it can only be accessed from the reverse proxy.

ep_sotauth

eqtl

Style guide for writing Ansible

nextflow-pipelines

Nextflow HGI pipelines

Nextflow

ansible-style-guide

bsub_jupyter_lab

start jupyterlab python and R server on LSF farm5 node via bsub

Python library for easily JSON encoding/decoding complex class-based Python models, using an arbitrarily complex (but easy to write!) mapping schema.

python-hgijson

CLI and Python interface for easily managing Consul locks

consul-lock

BridgeBuilder efficiently remaps BAM/SAM reads to a new reference by first building a "bridge" reference, first mapping to that bridge, and then remapping only a subset of reads to the full new reference.

bridgebuilder

Orchestration and configuration management of hgi systems (using terraform & ansible)

hgi-systems

HCL

arvados-pipelines

HGI arvados pipelines (crunch scripts, container Dockerfiles, pipeline templates, etc)

serapis

Serapis archival system

bsub Rstudio server on Sanger LSF farm, with access to /lustre, to be accessed via web browser

rstudio_sanger_lsf_farm

Efficiently lstat every file in a filesystem tree in parallel across multiple nodes using MPI.

mpistat

single_cell_annotation

Tools for managing GitLab CI pipeline build variables

gitlab-build-variables

bam2cram-check

hgi-web

Inside Your Genome Project

IYG

Userspace CRAM-to-BAM translation virtual filesystem

13amp

treeserve

C++

vareval

A collection of scripts for evaluating variant callers

Common Workflow Language

ldapvi

Clone of ldapvi from http://www.lichteblau.com/git/ldapvi.git

metadata-check

Tests to perform on the iRODS metadata for a BAM file, versus the information in the file header

Single cell RNA-seq quality control, transcription profile clustering & cell-type assignment

nf_scrna_qc

Wrapper script to allow non-root users to run privileged lfs commands on particular Lustre filesystems (using sudo)

lustre_operator

Perl

yatadis

Yet Another Terraform Ansible Dynamic Inventory Script (yatadis)

HAPI-UR: HAPlotype Inference for UnRelated samples (cloned from: https://code.google.com/p/hapi-ur)

hapi-ur

C++

webhook-router

A system that accepts incoming webhooks from the Internet and routes them to internal locations, depending on a configuration that can be dynamically modified by users

Vue

seq_autoqc

Additional high-throughput sequencing autoQC steps

docker-icat

iRODS server in a Docker container

Tools to view LSF hierarchical fairshare UserGroup shares and current priority (e.g. in a treemap)

www-hierarchical-fairshare

nf_scrna_deconvolution

CellSNP-Vireo deconvolution pipeline, with optional genotype input.

Nextflow

mercuryrc

HGI's materials for the EBI Next Generation Sequencing (NGS) workshop

ebi-ngs-workshop

TeX

helpful-genestack-scripts

Some useful scripts for use with genestack

Single Cell pipelines used at Sanger

single_cell

Convenience scripts for reading/creating the contents of .irodsA files

irodsa-utilities

Generates https://view.commonwl.org/ like workflows images, showing a complete workflow.

cwl-graph-generate

serapis-web

Data retention policy tools

hgi-vault

SSDV

Single cell Nextflow cellbender pipeline.

nf_cellbender

Node.js framework for hypr-based graph information systems

yggdrasil

Hail based analysis pipelines for HG projects

hail_analysis_pipelines

Ansible role for Fluent Bit

ansible-fluent-bit

baton in a Docker container

bindmapfuse

docker-baton

Extract a tar archive, defusing any tarbombs

coloc

tarbomb-disposal

A command line based secrets manager

secrets

docker image instructions for Indelible

indelible-docker

Dockerfile

genestack-uploader

A HTTP server providing an API and a frontend for easy uploading to Genestack

Gets information about what is in an OpenStack tenant

openstack-info

Quick tool to connect the HGI queues on RT to the MUC

shadowbroker

Scala

FPGA-Evaluation

A repository of scripts and other miscellaneous things for evaluating FPGA accelerated pipelines.

Wraps callables to capture stdout, stderr, exceptions and the return

python-capturewrap

Clone of git://git.nic.cz/python-rt.git

docker-cookhla

Dockerfile

python-rt

Service to sync GitHub and GitLab repositories

github-to-gitlab-hook

Human Genetics Programme project and team group registry API

hgi-registry

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

hgi-cloud