Pinned Repositories
analysis-wdls
Early stages of converting genome/analysis-workflows from CWL to WDL
arvados
an open source platform for managing and analyzing biomedical big data
bfx-workshop
cancer-genomics-workflow
Pilot test for using the Arvados system to create new MGI cancer pipelines.
civic-client
Web client for CIViC: Clinical Interpretations of Variants in Cancer
civic-docs
Source code for the civicdb.org docs
civic-server
Backend Server for CIViC Project
civic-v2
CIViC version 2 server & client projects
CIVIC_SVI_Course
A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines
cloud-automation
Automation for standing up Gen3 commons on AWS, GCP, Azure, and on-prem
tmooney's Repositories
tmooney/analysis-wdls
Early stages of converting genome/analysis-workflows from CWL to WDL
tmooney/bfx-workshop
tmooney/cancer-genomics-workflow
Pilot test for using the Arvados system to create new MGI cancer pipelines.
tmooney/civic-v2
CIViC version 2 server & client projects
tmooney/CIVIC_SVI_Course
A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines
tmooney/cloud-automation
Automation for standing up Gen3 commons on AWS, GCP, Azure, and on-prem
tmooney/cloud-workflows
Infrastructure and tooling required to get genomic workflows running in the cloud
tmooney/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
tmooney/docker-alignment_helper-cwl
tmooney/docker-checkstrandedness
tmooney/docker-fp_filter-cwl
This is the one used in current CWL pipelines - pulls from fpfilter-tool
tmooney/docker-mapq0-filter
filter a vcf for variants with high percentage of mapq0 reads
tmooney/docker-samtools
Docker container for Samtools
tmooney/docker-samtools-cwl
tmooney/gcs-inventory-loader
Load your GCS bucket inventory into BigQuery fast with this tool.
tmooney/genome
tmooney/immuno_gcp_wdl_compute1
Tutorial to run immuno.wdl on Google Cloud
tmooney/Immuno_Workflow_Course
tmooney/laims
tmooney/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
tmooney/ottr-reports
For report checks for OTTR Github Actions.
tmooney/OTTR_Template
OTTR: Open-source Tools for Training Resources. This is template repository for creating online courses to be published on multiple platforms. See here: https://jhudatascience.org/OTTR_Template/ for a rendered version.
tmooney/qc-analysis-pipeline
Workflow used for WGS data QC
tmooney/qc-metric-aggregator
Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.
tmooney/sequence-object-consolidator
Converts fields into a sequence object suitable for the analysis-wdls
tmooney/spectacle
tmooney/STAR-Fusion
STAR-Fusion codebase
tmooney/toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
tmooney/toy-wdl-output-test
A quick WDL workflow to produce some output structures.
tmooney/workflow_docs
How to get up and running use the oncology workflows