Discover umccr/cwl-ica Open Source project by UMCCR (@umccr)

🏺 Exploring novel tumor epitope identification

neoantigens

📊Evaluating, filtering, comparing, and visualising VCF

vcf_stuff

Jupyter Notebook

umccrise

🐍 DRAGEN Tumor/Normal workflow post-processing

Summary of a single or multiple MAF files.

MAF-summary

infrastructure

Infrastructure as Code at UMCCR

📚 Genomics Platform Group Reporter

gpgr

driver-analysis

Workflow for driver events identification across cohorts of tumours

RNAsum

Pipeline for generating RNAseq-based cancer patient reports

libica

🐍 Python SDK for Illumina Connected Analytics (ICA) 🐉

Visualise copy-number alterations and structural variants

CNV_SV-visualisation

sigrap

🎶 Wrappers for somatic mutation signature analysis tools

umccr-dictionary

UMCCR Data Dictionary

Rust+AWS+S3+Lambda+Noodles = Serverless Bioinformatics

s3-rust-noodles-bam

Nextflow pipeline and AWS stack for the GRIDSS/PURPLE/LINX toolkit

gridss-purple-linx-nf

Generate V2 SampleSheets from JSON Inputs

v2-samplesheet-maker

10x

🚀 10X dumping ground

Summary of TCGA datasets and steps for their harmonization.

TCGA-data-harmonization

sbeacon-exploration

Serverless Beacon v2 exploration for UMCCR use cases

Jupyter Notebook

orcabus

🐋 UMCCR Pipeline & Workflow Orchestration

🔆 Interacting with Illumina Connected Analytics (ICA) API

illumination

EJS

holmes

BAM fingerprint stack

A miscellaneous set of UMCCR dockerfiles that don't quite go anywhere else.

docker-who

Dockerfile

elsa-data

Genomic data sharing support software ("let the data go")

RNA-seq-analysis

Benchmarking different AWS Rust (vs non-Rust) client implementations

aws-benchmarks

A suite of secondary / tertiary functions for running ICA API calls

wrapica

UMCCR Beacon Documentation

beacon-doc

Jupyter Notebook

workflows

UMCCR production workflows

Some python/bash tools that can be used against the Holmes fingerprint database to help investigations

gen3-doc

UMCCR Gen3 Documentation

holmes-tools

A set of additional subcommands for icav2

icav2-cli-plugins

Reference data version tracking for UMCCR

reference_data

Pipelines for downloading and preparing TCGA data for analyses.

TCGA-data-prep

oncoanalyser

Nextflow

g3po

🤖 Assorted utility CLI to work with Gen3

UMCCR Data Portal Frontend

data-portal-client

UMCCR Data Portal API Backend in cloud native serverless

data-portal-apis

AWS Parallel Cluster setup for UMCCR

aws_parallel_cluster

Shell

hmftools-nf

A comprehensive cancer WGS/WTS analysis and reporting pipeline from the Hartwig Medical Foundation

Nextflow

bcl2fastq-docker

illumination-v2

Bioinformatics format (De)Serialization

linxreport

Linx Result Reporter

BioSerDe

Documentation for bcbio somatic variant calling

bcbio-varcall-doc

Shell

fake-passport-ecosystem

A fake GA4GH passport ecosystem that can be deployed to AWS, or run locally

Parsing Google-LIMS for dashboards and bcbio config files

google_lims

The CLI used for creating/syncing CWL workflows from GitHub to ICAv1

cwl-ica-cli