Ben Weisburd's repositories
ConfigArgParse
A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.
ExpansionHunter
A tool for estimating repeat sizes
hail-utils
misc. hail utils
hail-scripts
hail scripts from misc. analyses
actions-gh-pages
GitHub Actions for GitHub Pages 🚀 Deploy static files and publish your site easily. Static-Site-Generators-friendly.
annotation-utils
misc. python utilities
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
impute_sample_metadata
Hail Batch pipelines for imputing the reference genome version, sample type, etc. from BAM or CRAM files.
process_profiler
Runs in the background and records telemetry on running processes and system resources. Designed for instrumenting jobs in compute clusters.
step-pipeline
This library provides a thin wrapper API around Hail Batch that adds features like skipping steps whose output files have already been generated, additional options for localizing files, notifications about pipeline completion, etc.