exit and print error if kraken2_db not set

czbiohub-sf / sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

GNU Affero General Public License v3.0

25 stars 9 forks source link

exit and print error if kraken2_db not set #46

Open samlhao opened 4 years ago

samlhao commented 4 years ago

Right now, the pipeline will fail if skip_trim_adapters is not set but no kraken2 db is provided. There should be an explicit exit and error message if this happens.

jackkamm commented 3 years ago

Not sure if we ever resolved this, but closing it as stale; reopen a new issue if needed

danrlu commented 3 years ago

Can implement while migrating to DLS2