This WILDS WDL workflow downloads paired FASTQs from SRA and aligns them using the two-pass methodology of STAR. It is intended to be a relatively simplistic demonstration of an RNA sequencing pipeline within the context of the WILDS ecosystem.
For Fred Hutch users that are new to WDL, we recommend using PROOF to submit these workflows directly to the on-premise HPC cluster, as it simplifies interaction with Cromwell and provides a user-friendly front-end for job submission and tracking. For users outside of Fred Hutch or more advanced users who who would like to run the workflow locally, command line execution is relatively straightforward:
java -jar cromwell-86.jar run ww-sra-star.wdl --inputs ww-sra-star-inputs.json
Although Cromwell is demonstrated here, this pipeline is not specific to Cromwell and can be run using whichever WDL execution method you prefer (miniwdl, Terra, HealthOmics, etc.).
For questions, bugs, and/or feature requests, reach out to the Fred Hutch Data Science Lab (DaSL) at wilds@fredhutch.org, or open an issue on our issue tracker.
If you would like to contribute to this WILDS WDL workflow, see our contribution guidelines as well out our WILDS Contributor Guide for more details.
Distributed under the MIT License. See LICENSE for details.