getwilds/ww-fastq-to-cram

Self-contained WDL workflow that converts a WGS FASTQ file into an unmapped CRAM file

ww-fastq-to-cram

This WILDS WDL workflow converts a WGS FASTQ file into an unmapped CRAM file. While the FASTQ format is ubiquitous throughout the genomics community for raw sequencing data, unmapped CRAM files provide better lossless compression and allow additional metadata to be associated with each read. For more efficient and cost-effective archival data storage, we recommend conversion to this format using the relatively basic ww-fastq-to-cram WDL workflow.

Usage

For Fred Hutch users that are new to WDL, we recommend using PROOF to submit this workflow 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 straighforward:

java -jar cromwell-86.jar run ww-fastq-to-cram.wdl \
    --inputs ww-fastq-to-cram-inputs.json \
    --options ww-fastq-to-cram-options.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.).

Support

For questions, bugs, and/or feature requests, reach out to the Fred Hutch Data Science Lab (DaSL) at [email protected], or open an issue on our issue tracker.

Contributing

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.

License

Distributed under the MIT License. See LICENSE for details.