search

bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
19 stars 9 forks source link

Improve matam error management #7

Open ppericard opened 7 years ago

ppericard commented 7 years ago

Today, we just know if an error happened during a MATAM run, and at which step. Moreover, a MATAM run can keep on going even if there was a major problem in a previous step.

So predictable errors should be enumerated and dealt with, at least by printing them. And MATAM should not be able to start a step if the previous one had a major problem

loic-couderc commented 7 years ago

This issue is partially addressed by using the "logged_check_call" from 4ff82aaee04666a5ccc2b56602c03f3226220fcb. This method will terminate the pipeline execution when an error occurred.