Generate ora mount points by first recursively finding fastq files in the instrument run folder
Also generate a bash script for moving outputs to their new location post creation
Rather than trying to write bash code in CWL and handle bash variables, the move command is generated inside the typescript file and relies on the fastq list row generation and output directory name input to determine the source and destination paths of each ora to move.
Generate ora mount points by first recursively finding fastq files in the instrument run folder
Also generate a bash script for moving outputs to their new location post creation
Rather than trying to write bash code in CWL and handle bash variables, the move command is generated inside the typescript file and relies on the fastq list row generation and output directory name input to determine the source and destination paths of each ora to move.