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umccr / cwl-ica

A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide
MIT License
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ORA inputs to workflows (TN) require a --ora-reference input #582

Closed alexiswl closed 2 weeks ago

alexiswl commented 2 weeks ago

If fastq-list-rows are used and read1 or read2 exit, user must specify --ora-reference which is a directory.

If --ora-reference is specified on the CLI, script must first extract the reference directory into the scratch space, much like what is done for the current reference tar.

alexiswl commented 2 weeks ago

Resolved for TN, might want to add it in for WTS / dragen alignment pipelines though