Projects

R Packages

rcromwell
R client for interacting with Cromwell with WDL workflows
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.
sixtyfour
🚚 AWS for Data Scientists
Project Status: Prototype – Useable, some support, open to feedback, unstable API.
cancerprof
API Client for State Cancer Profiles
Project Status: Concept – Not useable, no support, not open to feedback, unstable API.
proofr
Client for the PROOF API
Project Status: Concept – Not useable, no support, not open to feedback, unstable API.
bs
Bootstrap Components for DASL Projects
Project Status: Concept – Not useable, no support, not open to feedback, unstable API.
rls
Row Level Security Functions for PostgreSQL and Redshift
Project Status: Concept – Not useable, no support, not open to feedback, unstable API.

Python Packages

Coming soon!

Docker Recipes

wilds-docker-library
Collection of Docker images for use in WILDS bioinformatics workflows
Project Status: Prototype – Useable, some support, open to feedback, unstable API.

Research Compendia

Coming soon!

WDLs

ww-sra-star
Workflow to download paired fastqs from SRA and pass through STAR 2 pass
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.
ww-cell-ranger
A basic starting point for a cell ranger workflow
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.
ww-star-deseq2
Relatively straightforward WDL workflow that executes STAR+DESeq2 on RNAseq data
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.
ww-fastq-to-cram
Self-contained WDL workflow that converts a WGS FASTQ file into an unmapped CRAM file
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.
ww-vc-trio
Variant calling WDL workflow using a trio of variant callers and analyzing consensus among them
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.
ww-sourmash
Self-contained WDL workflow that uses Sourmash to perform similarity searches between sequence files.
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.
ww-shapemapper
Self-contained WDL workflow that uses Shapemapper
Project Status: Experimental – Useable, some support, not open to feedback, unstable API.

NextFlow

Coming soon!

Repos status tally

Project Status: Experimental – Useable, some support, not open to feedback, unstable API.     8
Project Status: Prototype – Useable, some support, open to feedback, unstable API.     2
Project Status: Concept – Not useable, no support, not open to feedback, unstable API.     4