vortexing
Part-time Deputy Chief Data Officer, Part-time Translational Genomics Researcher, Full-time Data Science Enabler
Fred Hutchinson Cancer CenterSeattle, WA
Pinned Repositories
FH_Cluster201
An emerging course for effective use of FH Computing.
FH_WDL101_Cromwell
An introduction to using Cromwell and WDL at the Fred Hutch
diy-cromwell-server
A repo containing instructions for running a Cromwell server on Gizmo at the Fred Hutch. (Contact Amy Paguirigan for questions)
tgR.data
repo for TGR data management support package
wiki
SciWiki: Collective KnowledgeBase for Scientific Data and Use
rcromwell
R client for interacting with Cromwell with WDL workflows
bcftools-docker
bwa-docker
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
docker-conda-base
vortexing's Repositories
vortexing/bcftools-docker
vortexing/bwa-docker
vortexing/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
vortexing/docker-conda-base
vortexing/docker-gatk-samtools
gatk and updated samtools
vortexing/docker-gatk-samtools-bcftools
vortexing/docker-R-bioconductor
vortexing/docker-samtools
vortexing/docker-subset-bam
10x genomics subset bam docker setup/wdl
vortexing/docker-umi-star-sam
umi-tools, STAR aligner, samtools
vortexing/docker-vartrix
10x genomics vartrix docker/wdl setup
vortexing/easybuild-life-sciences
Howto and implementation documentation
vortexing/gatk
Official code repository for GATK versions 4 and up
vortexing/ichorCNA
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
vortexing/R-fetch-and-run-docker
vortexing/s3tagcrawler
search s3 based on tags
vortexing/slurm-examples
examples of using slurm in life sciences workflows using posix file systems and object storage
vortexing/star-docker
Docker container with STAR and samtools
vortexing/strelka-docker
strelka in docker
vortexing/umi-tools-docker
vortexing/vortexing.github.io
A short landing page for me.
vortexing/wdl
Workflow Description Language - Specification and Implementations