Hatem's repositories
nf-gcp-conf
Parametrised config file for Nextflow on Google Cloud Platform
configs
Config files used to define parameters specific to compute environments at different Institutions
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
cromwell-deployment
Scripts and configuration to setup a Cromwell deployment
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
parabricks-nextflow
Accelerated genomics workflows in NextFlow
rad-lab
RAD Lab enables users to deploy infrastructure on Google Cloud Platform (GCP) to support specific use cases. Infrastructure is created and managed through Terraform in conjunction with support scripts written in Python. The templates, code, and documentation for each use case are bundled into modules.
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
dsub
Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.
GoogleMAGs
Workflow for MAG construction
imcyto
Image Mass Cytometry analysis pipeline
nextflow
A DSL for data-driven computational pipelines
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
rnaseq-nf
A proof of concept of RNAseq pipeline
snakemake-executor-plugin-googlebatch
Snakemake executor plugin for Google Batch (under development)
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
wdl-runner
Easily run WDL workflows on GCP