moka-guys / automate_demultiplex

Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics
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newline in congenica run commands file required #512

Closed rebeccahaines1 closed 1 year ago

rebeccahaines1 commented 1 year ago

In release v44.8.0 some sections that added new lines in the dx run commands file were removed. However, this meant that in the Congenica run commands file the first command was not written to a new line, so this command couldn't be run. Add a new line ( + "\n") to this line https://github.com/moka-guys/automate_demultiplex/blob/c78c5ebda875deeac05917b8afa4757ac7c82708/upload_and_setoff_workflows.py#L2226