fix fluviewer log & error copying approach

BCCDC-PHL / fluviewer-nf

Nextflow pipeline for influenza A whole genome sequence analysis

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Closed jpalmer37 closed 2 months ago

jpalmer37 commented 2 months ago

jpalmer37 commented 2 months ago

Here's the new code structure:

SAVE_LOGS function will always run and rename appropriate logs / files in the logs folder of the work-dir
SAFE_EXIT function will only run upon non-zero fluviewer error status and forcefully copy the fluviewer*txt files under log to the outdir
under exit code 0, publishDir will capture the fluviewer*txt files