failPreExecution not running on fastq error
If fastqCountError or fastqReadError gets set as true (by getData process), then failPreExecution process should run to create the failed execution run with details. The process is currently set to wait for speciesError channel which doesn't get set till after inferMetadata process... but the fastq errors prevent that process from running, so failPreExecution run never happens.
Steps to reproduce
Run any replicate from study 16-2CNW
Observed bug behavior
Pipeline successful, but no execution run uploaded.
Pipeline successful, execution run uploaded with Error status and detail
Relevant logs and/or screenshots
Split failPreExecution process into 2 (1 dependent on the 2 fastq errors, the other dependent on species error)
THIS IS MY PREFERENECE BECAUSE OF EASE AND SPEED OF IMPLEMENTATION DSL2 will probably make this problem irrelevant anyway, so more complicated fix feels waste of time.
- make 1 error variable that any failure sets to true, then have failPreExecution dependent on only that variable