umccr/cwl-ica-cli

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Python
License
MIT License
Created about 2 years ago
Updated 4 months ago

umccr/cwl-ica-cli

umccr

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

htsget-rs

A server implementation of the htsget protocol for bioinformatics in Rust

neoantigens

🏺 Exploring novel tumor epitope identification

vcf_stuff

📊Evaluating, filtering, comparing, and visualising VCF

Jupyter Notebook

umccrise

🐍 DRAGEN Tumor/Normal workflow post-processing

MAF-summary

Summary of a single or multiple MAF files.

infrastructure

Infrastructure as Code at UMCCR

gpgr

📚 Genomics Platform Group Reporter

cwl-ica

A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide

Common Workflow Language

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) 🐉

CNV_SV-visualisation

Visualise copy-number alterations and structural variants

sigrap

🎶 Wrappers for somatic mutation signature analysis tools

umccr-dictionary

UMCCR Data Dictionary

s3-rust-noodles-bam

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

gridss-purple-linx-nf

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

v2-samplesheet-maker

Generate V2 SampleSheets from JSON Inputs

10x

🚀 10X dumping ground

TCGA-data-harmonization

Summary of TCGA datasets and steps for their harmonization.

sbeacon-exploration

Serverless Beacon v2 exploration for UMCCR use cases

Jupyter Notebook

orcabus

🐋 UMCCR Pipeline & Workflow Orchestration

illumination

🔆 Interacting with Illumina Connected Analytics (ICA) API

holmes

BAM fingerprint stack

docker-who

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

elsa-data

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

RNA-seq-analysis

aws-benchmarks

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

wrapica

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

beacon-doc

UMCCR Beacon Documentation

Jupyter Notebook

workflows

UMCCR production workflows

gen3-doc

UMCCR Gen3 Documentation

holmes-tools

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

icav2-cli-plugins

A set of additional subcommands for icav2

reference_data

Reference data version tracking for UMCCR

TCGA-data-prep

Pipelines for downloading and preparing TCGA data for analyses.

oncoanalyser

g3po

🤖 Assorted utility CLI to work with Gen3

data-portal-client

UMCCR Data Portal Frontend

data-portal-apis

UMCCR Data Portal API Backend in cloud native serverless

aws_parallel_cluster

AWS Parallel Cluster setup for UMCCR

hmftools-nf

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

bcl2fastq-docker

illumination-v2

linxreport

Linx Result Reporter

BioSerDe

Bioinformatics format (De)Serialization

bcbio-varcall-doc

Documentation for bcbio somatic variant calling

fake-passport-ecosystem

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

google_lims

Parsing Google-LIMS for dashboards and bcbio config files